Diff of the two buildlogs: -- --- b1/build.log 2023-07-23 05:57:53.311380451 +0000 +++ b2/build.log 2023-07-23 06:40:08.087467457 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Aug 24 00:01:42 -12 2024 -I: pbuilder-time-stamp: 1724500902 +I: Current time: Sun Jul 23 19:57:59 +14 2023 +I: pbuilder-time-stamp: 1690091879 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./sra-sdk_3.0.3+dfsg.orig.tar.xz] I: copying [./sra-sdk_3.0.3+dfsg-6~deb12u1.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Jul 14 09:42:24 2023 -12 +gpgv: Signature made Sat Jul 15 11:42:24 2023 +14 gpgv: using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sra-sdk_3.0.3+dfsg-6~deb12u1.dsc: no acceptable signature found @@ -40,135 +40,167 @@ dpkg-source: info: applying no_sse4.2.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/428083/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/556284/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 23 19:58 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/556284/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/556284/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='4e0de03298ee40e89b0d9b6c4311fb28' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='428083' - PS1='# ' - PS2='> ' + INVOCATION_ID=e23a8d4e4e474ed18afc20f3dc726cf5 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=556284 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3t3OzlOC/pbuilderrc_RhhU --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3t3OzlOC/b1 --logfile b1/build.log sra-sdk_3.0.3+dfsg-6~deb12u1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3t3OzlOC/pbuilderrc_XdH0 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3t3OzlOC/b2 --logfile b2/build.log sra-sdk_3.0.3+dfsg-6~deb12u1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-1 (2023-07-14) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-1 (2023-07-14) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/428083/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jul 23 19:58 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/556284/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -521,7 +553,7 @@ Get: 273 http://deb.debian.org/debian bookworm/main amd64 markdown all 1.0.1-12 [17.7 kB] Get: 274 http://deb.debian.org/debian bookworm/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 275 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] -Fetched 266 MB in 8s (31.8 MB/s) +Fetched 266 MB in 28s (9499 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19555 files and directories currently installed.) @@ -1824,7 +1856,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/sra-sdk-3.0.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../sra-sdk_3.0.3+dfsg-6~deb12u1_source.changes +I: user script /srv/workspace/pbuilder/556284/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/556284/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/sra-sdk-3.0.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../sra-sdk_3.0.3+dfsg-6~deb12u1_source.changes dpkg-buildpackage: info: source package sra-sdk dpkg-buildpackage: info: source version 3.0.3+dfsg-6~deb12u1 dpkg-buildpackage: info: source distribution bookworm @@ -2056,7 +2092,7 @@ make[1]: Leaving directory '/build/sra-sdk-3.0.3+dfsg' jh_linkjars -O--buildsystem=cmake dh_auto_build -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/sra-sdk-3.0.3+dfsg -B/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -2064,93 +2100,91 @@ make[2]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f shared/CMakeFiles/tk-version.dir/build.make shared/CMakeFiles/tk-version.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/shared /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared/CMakeFiles/tk-version.dir/DependInfo.cmake --color= make -f ngs/ncbi/ngs/CMakeFiles/ngs.dir/build.make ngs/ncbi/ngs/CMakeFiles/ngs.dir/depend -make -f ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build.make ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/depend +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/shared /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared/CMakeFiles/tk-version.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build.make ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/depend cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs/CMakeFiles/ngs.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/DependInfo.cmake --color= make -f ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build.make ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/depend +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/DependInfo.cmake --color= +make -f ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/build.make ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/DependInfo.cmake --color= -make -f ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/build.make ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/depend make -f ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build.make ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/DependInfo.cmake --color= -make -f ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build.make ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build.make ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/depend cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/DependInfo.cmake --color= -make -f ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build.make ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build.make ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/depend cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build.make ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/DependInfo.cmake --color= make -f shared/CMakeFiles/tk-version.dir/build.make shared/CMakeFiles/tk-version.dir/build +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/DependInfo.cmake --color= +make -f ngs/ngs-java/CMakeFiles/ngs-java.dir/build.make ngs/ngs-java/CMakeFiles/ngs-java.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f ngs/ngs-java/CMakeFiles/ngs-java.dir/build.make ngs/ngs-java/CMakeFiles/ngs-java.dir/depend +make -f ngs/ncbi/ngs/CMakeFiles/ngs.dir/build.make ngs/ncbi/ngs/CMakeFiles/ngs.dir/build make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build.make ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f ngs/ncbi/ngs/CMakeFiles/ngs.dir/build.make ngs/ncbi/ngs/CMakeFiles/ngs.dir/build -make -f ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build.make ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build +make -f ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build.make ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build.make ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build.make ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/build.make ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build.make ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build.make ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build.make ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build [ 0%] Building C object shared/CMakeFiles/tk-version.dir/toolkit.vers.c.o -make -f ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build.make ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"shared\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT shared/CMakeFiles/tk-version.dir/toolkit.vers.c.o -MF CMakeFiles/tk-version.dir/toolkit.vers.c.o.d -o CMakeFiles/tk-version.dir/toolkit.vers.c.o -c /build/sra-sdk-3.0.3+dfsg/shared/toolkit.vers.c +make -f ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build.make ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build.make ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build -[ 1%] Building C object ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build.make ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build make -f ngs/ngs-java/CMakeFiles/ngs-java.dir/build.make ngs/ngs-java/CMakeFiles/ngs-java.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-jni\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o -MF CMakeFiles/ngs-jni.dir/jni_Manager.c.o.d -o CMakeFiles/ngs-jni.dir/jni_Manager.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni/jni_Manager.c +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 0%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o -MF CMakeFiles/ngs.dir/NCBI-NGS.c.o.d -o CMakeFiles/ngs.dir/NCBI-NGS.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NCBI-NGS.c +[ 1%] Building C object ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o +[ 1%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o [ 1%] Building C object ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-jni\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o -MF CMakeFiles/ngs-jni.dir/jni_Manager.c.o.d -o CMakeFiles/ngs-jni.dir/jni_Manager.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni/jni_Manager.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong 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-I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o -MF CMakeFiles/ngs-py.dir/py_Manager.c.o.d -o CMakeFiles/ngs-py.dir/py_Manager.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py/py_Manager.c +[ 1%] Building C object ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g 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CMakeFiles/ngs-py.dir/py_Manager.c.o.d -o CMakeFiles/ngs-py.dir/py_Manager.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py/py_Manager.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o -MF CMakeFiles/ngs.dir/CSRA1_Pileup.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Pileup.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Pileup.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadCollection.cpp +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadCollectionItf.cpp [ 2%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadCollectionItf.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o -MF CMakeFiles/ngs.dir/CSRA1_Alignment.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Alignment.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Alignment.c +[ 2%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o [ 2%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentItf.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReadCollectionItf.cpp [ 2%] Building Java objects for ngs-java.jar cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClearClassFiles.cmake @@ -2159,19 +2193,25 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/javac -classpath :/build/sra-sdk-3.0.3+dfsg/ngs/ngs-java:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -d /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -h ./jni @/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_sources In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadCollectionItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadCollectionItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/javac -classpath :/build/sra-sdk-3.0.3+dfsg/ngs/ngs-java:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -d /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -h ./jni @/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_sources +[ 2%] Linking C static library ../ilib/libtk-version.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cmake -P CMakeFiles/tk-version.dir/cmake_clean_target.cmake +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cmake -E cmake_link_script CMakeFiles/tk-version.dir/link.txt --verbose=1 +/usr/bin/ar qc ../ilib/libtk-version.a "CMakeFiles/tk-version.dir/toolkit.vers.c.o" +[ 3%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o +/usr/bin/ranlib ../ilib/libtk-version.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o -MF CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o.d -o CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_ReferenceWindow.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/AlignmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 2%] Linking C static library ../ilib/libtk-version.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cmake -P CMakeFiles/tk-version.dir/cmake_clean_target.cmake +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -2186,406 +2226,210 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReferenceSequence.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceSequence.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 3%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o -MF CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o.d -o CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_ReferenceWindow.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cmake -E cmake_link_script CMakeFiles/tk-version.dir/link.txt --verbose=1 -/usr/bin/ar qc ../ilib/libtk-version.a "CMakeFiles/tk-version.dir/toolkit.vers.c.o" -/usr/bin/ranlib ../ilib/libtk-version.a -[ 3%] Linking C static library ../../../ilib/libngs-py.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py && /usr/bin/cmake -P CMakeFiles/ngs-py.dir/cmake_clean_target.cmake -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 3%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceItf.cpp -[ 4%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-py.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/PileupItf.cpp -[ 4%] Built target tk-version +[ 3%] Built target tk-version make -f ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/DependInfo.cmake --color= -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceItf.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -/usr/bin/ar qc ../../../ilib/libngs-py.a "CMakeFiles/ngs-py.dir/py_Manager.c.o" -[ 4%] Linking C static library ../../../ilib/libngs-jni.a -/usr/bin/ranlib ../../../ilib/libngs-py.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cmake -P CMakeFiles/ngs-jni.dir/cmake_clean_target.cmake -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 3%] Linking C static library ../../../ilib/libngs-py.a +[ 4%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py && /usr/bin/cmake -P CMakeFiles/ngs-py.dir/cmake_clean_target.cmake +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/PileupItf.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/build +[ 4%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/PileupEventItf.cpp cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/javadoc -d /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc -sourcepath "/build/sra-sdk-3.0.3+dfsg/ngs/ngs-java" gov.nih.nlm.ncbi.ngs ngs -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-jni.dir/link.txt --verbose=1 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-py.dir/link.txt --verbose=1 +/usr/bin/ar qc ../../../ilib/libngs-py.a "CMakeFiles/ngs-py.dir/py_Manager.c.o" +/usr/bin/ranlib ../../../ilib/libngs-py.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 4%] Built target ngs-py make -f libs/kxml/CMakeFiles/kxml.dir/build.make libs/kxml/CMakeFiles/kxml.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/kxml /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml/CMakeFiles/kxml.dir/DependInfo.cmake --color= -/usr/bin/ar qc ../../../ilib/libngs-jni.a "CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "CMakeFiles/ngs-jni.dir/jni_String.c.o" "CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" -/usr/bin/ranlib ../../../ilib/libngs-jni.a -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 4%] Linking C static library ../../../ilib/libngs-jni.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cmake -P CMakeFiles/ngs-jni.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/kxml/CMakeFiles/kxml.dir/build.make libs/kxml/CMakeFiles/kxml.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-jni.dir/link.txt --verbose=1 +[ 4%] Building C object libs/kxml/CMakeFiles/kxml.dir/xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/kxml/CMakeFiles/kxml.dir/xml.c.o -MF CMakeFiles/kxml.dir/xml.c.o.d -o CMakeFiles/kxml.dir/xml.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/kxml/xml.c +/usr/bin/ar qc ../../../ilib/libngs-jni.a "CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "CMakeFiles/ngs-jni.dir/jni_String.c.o" "CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" +/usr/bin/ranlib ../../../ilib/libngs-jni.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 4%] Built target ngs-jni make -f libs/loader/CMakeFiles/loader.dir/build.make libs/loader/CMakeFiles/loader.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg 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CMakeFiles/kxml.dir/xml.c.o.d -o CMakeFiles/kxml.dir/xml.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/kxml/xml.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/loader/CMakeFiles/loader.dir/build.make libs/loader/CMakeFiles/loader.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 4%] Building C object libs/loader/CMakeFiles/loader.dir/progressbar.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 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CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Reference.cpp -[ 5%] Building C object libs/loader/CMakeFiles/loader.dir/loader-file.c.o +[ 4%] Building C object libs/loader/CMakeFiles/loader.dir/loader-file.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/loader-file.c.o -MF CMakeFiles/loader.dir/loader-file.c.o.d -o CMakeFiles/loader.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/loader-file.c +[ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o -MF CMakeFiles/ngs.dir/CSRA1_Reference.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Reference.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Reference.c +[ 4%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReferenceItf.cpp /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReadCollectionItf; C = NGS_ReadCollection_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Reference.cpp:27: +[ 4%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReferenceSequenceItf.cpp +[ 4%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/AlignmentItf.cpp +[ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o -MF CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_ReadCollection.c +[ 4%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceSequence.cpp +[ 4%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceIteratorItf.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceIteratorItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReferenceIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceIterator.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReferenceItf; C = NGS_Reference_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 106 | if ( this == 0 ) - | ^~ -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReferenceItf; C = NGS_Reference_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 100 | if ( this == 0 ) - | ^~ -[ 5%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceIteratorItf.cpp -[ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o -MF CMakeFiles/ngs.dir/CSRA1_Reference.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Reference.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Reference.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceIteratorItf.cpp:31: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReferenceSequence.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceSequence.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 5%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceSequenceItf.cpp -[ 5%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o +[ 4%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentIteratorItf.cpp -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceSequenceItf.cpp:27: +[ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o -MF CMakeFiles/ngs.dir/CSRA1_Read.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Read.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Read.c +[ 4%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceItf.cpp +[ 4%] Building C object libs/loader/CMakeFiles/loader.dir/loader-meta.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/loader-meta.c.o -MF CMakeFiles/loader.dir/loader-meta.c.o.d -o CMakeFiles/loader.dir/loader-meta.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/loader-meta.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 5%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/PileupEventItf.cpp -[ 5%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o +Loading source files for package gov.nih.nlm.ncbi.ngs... In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/AlignmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReferenceItf.cpp -[ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o -MF CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_ReadCollection.c -[ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o -MF CMakeFiles/ngs.dir/CSRA1_Read.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Read.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Read.c -[ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/EBI_ReferenceSequence.c -[ 5%] Building C object libs/loader/CMakeFiles/loader.dir/loader-meta.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/loader-meta.c.o -MF CMakeFiles/loader.dir/loader-meta.c.o.d -o CMakeFiles/loader.dir/loader-meta.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/loader-meta.c -[ 5%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupIterator.cpp -[ 5%] Building C object libs/loader/CMakeFiles/loader.dir/queue-file.c.o +Loading source files for package ngs... +[ 4%] Building C object libs/kxml/CMakeFiles/kxml.dir/xtoc-parsexml.c.o +[ 4%] Building C object libs/loader/CMakeFiles/loader.dir/queue-file.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/queue-file.c.o -MF CMakeFiles/loader.dir/queue-file.c.o.d -o CMakeFiles/loader.dir/queue-file.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/queue-file.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Pileup.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupIterator.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/kxml/CMakeFiles/kxml.dir/xtoc-parsexml.c.o -MF CMakeFiles/kxml.dir/xtoc-parsexml.c.o.d -o CMakeFiles/kxml.dir/xtoc-parsexml.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/kxml/xtoc-parsexml.c +[ 4%] Building C object libs/loader/CMakeFiles/loader.dir/alignment-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/alignment-writer.c.o -MF CMakeFiles/loader.dir/alignment-writer.c.o.d -o CMakeFiles/loader.dir/alignment-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/alignment-writer.c +[ 4%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReadGroupItf.cpp +[ 4%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReadItf.cpp +[ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/EBI_ReferenceSequence.c +[ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o -MF CMakeFiles/ngs.dir/SRA_Statistics.c.o.d -o CMakeFiles/ngs.dir/SRA_Statistics.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_Statistics.c -[ 5%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Pileup.cpp +Constructing Javadoc information... +[ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o -MF CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_DB_ReadCollection.c +[ 5%] Building C object libs/loader/CMakeFiles/loader.dir/common-reader.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/common-reader.c.o -MF CMakeFiles/loader.dir/common-reader.c.o.d -o CMakeFiles/loader.dir/common-reader.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/common-reader.c [ 5%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceItf.cpp -Loading source files for package gov.nih.nlm.ncbi.ngs... +[ 5%] Building C object libs/kxml/CMakeFiles/kxml.dir/xtoc.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/kxml/CMakeFiles/kxml.dir/xtoc.c.o -MF CMakeFiles/kxml.dir/xtoc.c.o.d -o CMakeFiles/kxml.dir/xtoc.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/kxml/xtoc.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -Loading source files for package ngs... -[ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Pileup.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Pileup.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o -MF CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_DB_ReadCollection.c -[ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o +[ 6%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceIterator.cpp +[ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o -MF CMakeFiles/ngs.dir/SRA_Read.c.o.d -o CMakeFiles/ngs.dir/SRA_Read.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_Read.c -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReferenceSequenceItf; C = NGS_ReferenceSequence_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 106 | if ( this == 0 ) - | ^~ -[ 5%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o +[ 6%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentItf.cpp -[ 5%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o -[ 5%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReferenceSequenceItf.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PileupItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PileupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupItf.cpp -[ 5%] Building C object libs/kxml/CMakeFiles/kxml.dir/xtoc-parsexml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/kxml/CMakeFiles/kxml.dir/xtoc-parsexml.c.o -MF CMakeFiles/kxml.dir/xtoc-parsexml.c.o.d -o CMakeFiles/kxml.dir/xtoc-parsexml.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/kxml/xtoc-parsexml.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupItf.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o -MF CMakeFiles/ngs.dir/SRA_ReadGroup.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadGroup.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadGroup.c -[ 5%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupEventItf.cpp -[ 5%] Building C object libs/loader/CMakeFiles/loader.dir/alignment-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/alignment-writer.c.o -MF CMakeFiles/loader.dir/alignment-writer.c.o.d -o CMakeFiles/loader.dir/alignment-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/alignment-writer.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupEventItf.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | +[ 6%] Building C object libs/loader/CMakeFiles/loader.dir/common-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/common-writer.c.o -MF CMakeFiles/loader.dir/common-writer.c.o.d -o CMakeFiles/loader.dir/common-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/common-writer.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 5%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/AlignmentItf.cpp -Constructing Javadoc information... -[ 5%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEventIterator.cpp -[ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o -MF CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadGroupInfo.c -[ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o -MF CMakeFiles/ngs.dir/SRA_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadCollection.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadCollection.c -[ 6%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o -[ 7%] Building C object libs/loader/CMakeFiles/loader.dir/common-reader.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEvent.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/common-reader.c.o -MF CMakeFiles/loader.dir/common-reader.c.o.d -o CMakeFiles/loader.dir/common-reader.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/common-reader.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEventIterator.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::PileupEventItf; C = NGS_PileupEvent_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 106 | if ( this == 0 ) - | ^~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReferenceSequence.c -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::PileupEventItf; C = NGS_PileupEvent_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 100 | if ( this == 0 ) - | ^~ -[ 7%] Building C object libs/kxml/CMakeFiles/kxml.dir/xtoc.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/kxml/CMakeFiles/kxml.dir/xtoc.c.o -MF CMakeFiles/kxml.dir/xtoc.c.o.d -o CMakeFiles/kxml.dir/xtoc.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/kxml/xtoc.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEvent.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReferenceIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 7%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceSequenceItf.cpp -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::PileupItf; C = NGS_Pileup_v1]': +[ 6%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/FragmentItf.cpp +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReferenceItf; C = NGS_Reference_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::PileupItf; C = NGS_Pileup_v1]': +[ 6%] Building C object libs/loader/CMakeFiles/loader.dir/mmarray.c.o +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReferenceItf; C = NGS_Reference_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceSequenceItf.cpp:31: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o -MF CMakeFiles/ngs.dir/NGS_Statistics.c.o.d -o CMakeFiles/ngs.dir/NGS_Statistics.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Statistics.c -[ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o -MF CMakeFiles/ngs.dir/NGS_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/NGS_ReadCollection.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReadCollection.c -[ 7%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReadGroupItf.cpp -[ 7%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupIteratorItf.cpp -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupIteratorItf.cpp:31: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 7%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o -MF CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/AlignmentItf.cpp -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/AlignmentItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/AlignmentItf.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 8%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadGroupItf.cpp -[ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o -[ 8%] Building C object libs/loader/CMakeFiles/loader.dir/common-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o -MF CMakeFiles/ngs.dir/NGS_PileupEvent.c.o.d -o CMakeFiles/ngs.dir/NGS_PileupEvent.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_PileupEvent.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/common-writer.c.o -MF CMakeFiles/loader.dir/common-writer.c.o.d -o CMakeFiles/loader.dir/common-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/common-writer.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadGroupItf.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 8%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentIteratorItf.cpp -[ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o -MF CMakeFiles/ngs.dir/NGS_Pileup.c.o.d -o CMakeFiles/ngs.dir/NGS_Pileup.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Pileup.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentIteratorItf.cpp:30: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/mmarray.c.o -MF CMakeFiles/loader.dir/mmarray.c.o.d -o CMakeFiles/loader.dir/mmarray.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/mmarray.c +[ 7%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/StatisticsItf.cpp +[ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o -MF CMakeFiles/ngs.dir/SRA_ReadGroup.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadGroup.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadGroup.c +[ 7%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/StringItf.cpp +[ 7%] Building C object libs/loader/CMakeFiles/loader.dir/reference-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/reference-writer.c.o -MF CMakeFiles/loader.dir/reference-writer.c.o.d -o CMakeFiles/loader.dir/reference-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/reference-writer.c +[ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o -MF CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadGroupInfo.c Creating destination directory: "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/" Building index for all the packages and classes... -[ 8%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o +[ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReferenceSequence.c +[ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o -MF CMakeFiles/ngs.dir/SRA_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadCollection.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadCollection.c Standard Doclet version 17.0.7+7-Debian-1deb12u1 Building tree for all the packages and classes... -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReadItf.cpp -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReadGroupItf; C = NGS_ReadGroup_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 106 | if ( this == 0 ) - | ^~ -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReadGroupItf; C = NGS_ReadGroup_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 100 | if ( this == 0 ) - | ^~ -[ 8%] Linking C static library ../../ilib/libkxml.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cmake -P CMakeFiles/kxml.dir/cmake_clean_target.cmake -[ 8%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cmake -E cmake_link_script CMakeFiles/kxml.dir/link.txt --verbose=1 -/usr/bin/ar qc ../../ilib/libkxml.a CMakeFiles/kxml.dir/xml.c.o "CMakeFiles/kxml.dir/xtoc-parsexml.c.o" CMakeFiles/kxml.dir/xtoc.c.o -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp:31: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 8%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o +[ 8%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentIteratorItf.cpp Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Alignment.html... -/usr/bin/ranlib ../../ilib/libkxml.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/FragmentItf.cpp -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 8%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/AlignmentIterator.cpp -[ 8%] Built target kxml -make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/depend -[ 8%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Alignment.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o -MF CMakeFiles/ngs.dir/NGS_ReadGroup.c.o.d -o CMakeFiles/ngs.dir/NGS_ReadGroup.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReadGroup.c -[ 9%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o -MF CMakeFiles/ngs.dir/NGS_Alignment.c.o.d -o CMakeFiles/ngs.dir/NGS_Alignment.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Alignment.c -[ 9%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReadItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReadItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadItf.cpp -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadItf.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 9%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Alignment.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/vdb-sqlite\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o -MF CMakeFiles/vdb-sqlite.dir/sqlite3.c.o.d -o CMakeFiles/vdb-sqlite.dir/sqlite3.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/AlignmentIterator.cpp:27: +[ 8%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/Refcount.cpp +[ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o -MF CMakeFiles/ngs.dir/NGS_Statistics.c.o.d -o CMakeFiles/ngs.dir/NGS_Statistics.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Statistics.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +[ 8%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Reference.cpp +[ 8%] Building C object libs/loader/CMakeFiles/loader.dir/sequence-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/sequence-writer.c.o -MF CMakeFiles/loader.dir/sequence-writer.c.o.d -o CMakeFiles/loader.dir/sequence-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/sequence-writer.c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:217: warning: @return has already been specified * @return '-' if negative strand is transcribed ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:218: warning: @return has already been specified * @return '?' if unknown ^ -[ 9%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventIteratorItf.cpp -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::AlignmentItf; C = NGS_Alignment_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 106 | if ( this == 0 ) - | ^~ -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::AlignmentItf; C = NGS_Alignment_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 100 | if ( this == 0 ) - | ^~ -[ 9%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o -MF CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/FragmentItf.cpp +[ 8%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ErrorMsg.cpp +[ 8%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceSequenceItf.cpp /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:140: warning: no comment static int all = primaryAlignment | secondaryAlignment; ^ @@ -2600,26 +2444,18 @@ ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:131: warning: no comment static int minMapQuality = 4; // pass alignments with mappingQuality >= param -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/FragmentItf.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:133: warning: no comment static int noWraparound = 16; // do not include leading wrapped around alignments to circular references ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:130: warning: no comment +[ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o -MF CMakeFiles/ngs.dir/NGS_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/NGS_ReadCollection.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReadCollection.c static int passDuplicates = 2; // either a PCR or optical duplicate ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:129: warning: no comment static int passFailed = 1; // reads rejected due to platform/vendor quality criteria ^ -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventIteratorItf.cpp:31: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:138: warning: no comment static int primaryAlignment = 1; ^ @@ -2629,58 +2465,65 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:134: warning: no comment static int startWithinSlice = 32; // change slice intersection criteria so that start pos is within slice ^ -[ 10%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PackageItf.cpp -[ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o -MF CMakeFiles/ngs.dir/NGS_Reference.c.o.d -o CMakeFiles/ngs.dir/NGS_Reference.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Reference.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceSequenceItf.cpp:31: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PackageItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PackageItf.cpp:30: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Reference.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp:38:7: warning: 'jlong Cast(ngs::PileupEventItf*)' defined but not used [-Wunused-function] - 38 | jlong Cast ( PileupEventItf * obj ) - | ^~~~ -[ 11%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/StatisticsItf.cpp -[ 11%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/StringItf.cpp -[ 11%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReadItf; C = NGS_Read_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 106 | if ( this == 0 ) - | ^~ -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReadItf; C = NGS_Read_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 100 | if ( this == 0 ) - | ^~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroupIterator.cpp +[ 8%] Linking C static library ../../ilib/libkxml.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cmake -P CMakeFiles/kxml.dir/cmake_clean_target.cmake +[ 8%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cmake -E cmake_link_script CMakeFiles/kxml.dir/link.txt --verbose=1 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ErrBlock.cpp +/usr/bin/ar qc ../../ilib/libkxml.a CMakeFiles/kxml.dir/xml.c.o "CMakeFiles/kxml.dir/xtoc-parsexml.c.o" CMakeFiles/kxml.dir/xtoc.c.o +/usr/bin/ranlib ../../ilib/libkxml.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 8%] Built target kxml +make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/DependInfo.cmake --color= +[ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o -MF CMakeFiles/ngs.dir/NGS_PileupEvent.c.o.d -o CMakeFiles/ngs.dir/NGS_PileupEvent.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_PileupEvent.c +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 8%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceSequenceItf.cpp +[ 8%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/vdb-sqlite\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o -MF CMakeFiles/vdb-sqlite.dir/sqlite3.c.o.d -o CMakeFiles/vdb-sqlite.dir/sqlite3.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c +[ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o -MF CMakeFiles/ngs.dir/NGS_Pileup.c.o.d -o CMakeFiles/ngs.dir/NGS_Pileup.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Pileup.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceSequenceItf.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 8%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupIterator.cpp Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/AlignmentIterator.html... +Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ErrorMsg.html... In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroupIterator.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Pileup.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::FragmentItf; C = NGS_Fragment_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 106 | if ( this == 0 ) - | ^~ -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::FragmentItf; C = NGS_Fragment_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 100 | if ( this == 0 ) - | ^~ -Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ErrorMsg.html... /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/ErrorMsg.java:49: warning: no comment public ErrorMsg () ^ @@ -2691,14 +2534,11 @@ public ErrorMsg ( ErrorMsg obj ) ^ Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Fragment.html... -[ 11%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventItf.cpp +[ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o +[ 9%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o -MF CMakeFiles/ngs.dir/NGS_ReadGroup.c.o.d -o CMakeFiles/ngs.dir/NGS_ReadGroup.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReadGroup.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PackageItf.cpp Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/FragmentIterator.html... -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventItf.cpp:31: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html... /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:29: warning: no comment public class LibDependencies { @@ -2709,49 +2549,47 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:30: warning: no comment public final static String NGS_SDK = "ngs-sdk"; ^ -[ 12%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html... -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroup.cpp -[ 12%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceSequence.c -[ 13%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:40: warning: no comment -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentIteratorItf.cpp public class NGS ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:133: warning: no comment public static void main(String[] args) { +[ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ^ -[ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o -MF CMakeFiles/ngs.dir/NGS_Read.c.o.d -o CMakeFiles/ngs.dir/NGS_Read.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Read.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentIteratorItf.cpp:31: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -Note: ngs/itf/Refcount.java uses or overrides a deprecated API. -Note: Recompile with -Xlint:deprecation for details. +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o -MF CMakeFiles/ngs.dir/NGS_Alignment.c.o.d -o CMakeFiles/ngs.dir/NGS_Alignment.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Alignment.c +[ 10%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupIteratorItf.cpp +[ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o -MF CMakeFiles/ngs.dir/NGS_Reference.c.o.d -o CMakeFiles/ngs.dir/NGS_Reference.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Reference.c Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Package.html... -Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Pileup.html... -cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/cmake -E touch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_compiled_ngs-java -[ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o -MF CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StatisticsItf.cpp +[ 10%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroup.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PackageItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PackageItf.cpp:30: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupIteratorItf.cpp:31: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Pileup.html... +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEvent.html... +[ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:118: warning: no comment static int alignment_minus_strand = 0x20; ^ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceSequence.c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:116: warning: no comment static int alignment_start = 0x80; ^ @@ -2759,20 +2597,17 @@ static int alignment_stop = 0x40; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:98: warning: no comment +[ 10%] Linking CXX static library ../../../ilib/libngs-adapt-c++.a static int deletion = 2; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:104: warning: no comment -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StatisticsItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StatisticsItf.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | static int insertion = 0x08; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:112: warning: no comment static int insertion_before_deletion = insertion | deletion; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:107: warning: no comment +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/cmake -P CMakeFiles/ngs-adapt-c++.dir/cmake_clean_target.cmake static int insertion_before_match = insertion | match; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:108: warning: no comment @@ -2799,19 +2634,13 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:113: warning: no comment static int replacement = insertion_before_deletion; ^ -[ 13%] Generating CMakeFiles/ngs-java.dir/java_class_filelist -cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClassFilelist.cmake -[ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PackageItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PackageItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PackageItf.cpp -[ 13%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/Refcount.cpp -[ 13%] Creating Java archive ngs-java.jar +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-adapt-c++.dir/link.txt --verbose=1 Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEventIterator.html... -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir && /usr/bin/jar -cf /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar @java_class_filelist -[ 13%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ErrorMsg.cpp +/usr/bin/ar qc ../../../ilib/libngs-adapt-c++.a "CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o" +/usr/bin/ranlib ../../../ilib/libngs-adapt-c++.a Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupIterator.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Read.html... +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:35: warning: no comment public interface Read ^ @@ -2822,47 +2651,45 @@ static int all = aligned | unaligned; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:78: warning: no comment +[ 10%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o static int partiallyAligned = 2; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:80: warning: no comment static int unaligned = 4; ^ -[ 13%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PackageItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PackageItf.cpp:27: +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Pileup.cpp +[ 10%] Built target ngs-adapt-c++ +make -f libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build.make libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/DependInfo.cmake --color= +[ 10%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventIteratorItf.cpp +Note: ngs/itf/Refcount.java uses or overrides a deprecated API. +Note: Recompile with -Xlint:deprecation for details. +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventIteratorItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventItf.cpp -[ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o -MF CMakeFiles/ngs.dir/NGS_Fragment.c.o.d -o CMakeFiles/ngs.dir/NGS_Fragment.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Fragment.c -[ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o -MF CMakeFiles/ngs-disp.dir/StringItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/StringItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build.make libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Pileup.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Pileup.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +[ 10%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReadCollection.cpp +cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/cmake -E touch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_compiled_ngs-java Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadCollection.html... -[ 13%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadIterator.cpp -[ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o -MF CMakeFiles/ngs.dir/NGS_Cursor.c.o.d -o CMakeFiles/ngs.dir/NGS_Cursor.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Cursor.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventItf.cpp:30: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroup.html... -Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroupIterator.html... -Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadIterator.html... -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/ReadIterator.java:34: warning: no comment -public interface ReadIterator - ^ -Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Reference.html... +[ 10%] Generating CMakeFiles/ngs-java.dir/java_class_filelist +cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClassFilelist.cmake In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -2870,11 +2697,26 @@ from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadIterator.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, + from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReadCollection.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::StatisticsItf; C = NGS_Statistics_v1]': +Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroup.html... +[ 10%] Creating Java archive ngs-java.jar +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir && /usr/bin/jar -cf /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar @java_class_filelist +Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroupIterator.html... +Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadIterator.html... +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/ReadIterator.java:34: warning: no comment +public interface ReadIterator + ^ +Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Reference.html... +[ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o -MF CMakeFiles/ngs.dir/NGS_Read.c.o.d -o CMakeFiles/ngs.dir/NGS_Read.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Read.c +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReferenceSequenceItf; C = NGS_ReferenceSequence_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ @@ -2896,131 +2738,285 @@ Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/package-summary.html... -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=ngs-java.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.25/Modules/UseJava/Symlinks.cmake +[ 10%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/package-tree.html... -[ 13%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventItf.cpp Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/constant-values.html... -[ 13%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentItf.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupIteratorItf.cpp -[ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o -MF CMakeFiles/ngs.dir/NGS_Refcount.c.o.d -o CMakeFiles/ngs.dir/NGS_Refcount.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Refcount.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventItf.cpp:31: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/serialized-form.html... -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/overview-tree.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/index.html... -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupIteratorItf.cpp:30: +[ 10%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEventIterator.cpp +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp:38:7: warning: 'jlong Cast(ngs::PileupEventItf*)' defined but not used [-Wunused-function] + 38 | jlong Cast ( PileupEventItf * obj ) + | ^~~~ +[ 10%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PileupItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PileupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupItf.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +Building index for all classes... +Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/allclasses-index.html... +Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/allpackages-index.html... +Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/index-all.html... +[ 10%] Linking C static library ../../ilib/libloader.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cmake -P CMakeFiles/loader.dir/cmake_clean_target.cmake +[ 11%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentIteratorItf.cpp +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=ngs-java.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.25/Modules/UseJava/Symlinks.cmake +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/loader.dir/link.txt --verbose=1 +[ 11%] Built target ngs-java +make -f libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build.make libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/depend +/usr/bin/ar qc ../../ilib/libloader.a CMakeFiles/loader.dir/progressbar.c.o "CMakeFiles/loader.dir/loader-file.c.o" "CMakeFiles/loader.dir/loader-meta.c.o" "CMakeFiles/loader.dir/queue-file.c.o" "CMakeFiles/loader.dir/alignment-writer.c.o" "CMakeFiles/loader.dir/common-reader.c.o" "CMakeFiles/loader.dir/common-writer.c.o" CMakeFiles/loader.dir/mmarray.c.o "CMakeFiles/loader.dir/reference-writer.c.o" "CMakeFiles/loader.dir/sequence-writer.c.o" +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/DependInfo.cmake --color= +[ 11%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentItf.cpp:31: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentIteratorItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 13%] Built target ngs-java -make -f libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build.make libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/DependInfo.cmake --color= -Building index for all classes... +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEventIterator.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventItf.cpp +/usr/bin/ranlib ../../ilib/libloader.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build.make libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build -Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/allclasses-index.html... +make -f libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build.make libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/allpackages-index.html... -Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/index-all.html... -[ 13%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o -[ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o -[ 13%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReadCollection.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Read.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Read.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Read.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o -MF CMakeFiles/ngs-disp.dir/Refcount.cpp.o.d -o CMakeFiles/ngs-disp.dir/Refcount.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp: In member function 'const char* ngs::StringItf::data() const': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:62:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 62 | if ( this != 0 ) - | ^~ -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp: In member function 'size_t ngs::StringItf::size() const': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:97:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 97 | if ( this != 0 ) - | ^~ -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::StringItf; C = NGS_String_v1]': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 106 | if ( this == 0 ) - | ^~ +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/overview-summary.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/help-doc.html... -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:27: +[ 11%] Building CXX object libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o -MF CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o.d -o CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_makedb.cpp +[ 11%] Built target loader +make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ascp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp/CMakeFiles/ascp.dir/DependInfo.cmake --color= +46 warnings +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 11%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o -MF CMakeFiles/ngs.dir/NGS_Fragment.c.o.d -o CMakeFiles/ngs.dir/NGS_Fragment.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Fragment.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 13%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o -46 warnings -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ErrBlock.cpp -[ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o +[ 11%] Building C object libs/ascp/CMakeFiles/ascp.dir/ascp.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/sra-sdk-3.0.3+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/ascp/CMakeFiles/ascp.dir/ascp.c.o -MF CMakeFiles/ascp.dir/ascp.c.o.d -o CMakeFiles/ascp.dir/ascp.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/ascp/ascp.c +[ 11%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o -MF CMakeFiles/ngs.dir/NGS_Cursor.c.o.d -o CMakeFiles/ngs.dir/NGS_Cursor.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Cursor.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 11%] Built target ngs-doc_javadoc +make -f libs/diagnose/CMakeFiles/diagnose.dir/build.make libs/diagnose/CMakeFiles/diagnose.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/diagnose /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose/CMakeFiles/diagnose.dir/DependInfo.cmake --color= +[ 11%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o -MF CMakeFiles/ngs.dir/NGS_Refcount.c.o.d -o CMakeFiles/ngs.dir/NGS_Refcount.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Refcount.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f libs/diagnose/CMakeFiles/diagnose.dir/build.make libs/diagnose/CMakeFiles/diagnose.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 11%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o +[ 11%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEvent.cpp +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/sra-sdk-3.0.3+dfsg/libs/diagnose -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o -MF CMakeFiles/diagnose.dir/diagnose.c.o.d -o CMakeFiles/diagnose.dir/diagnose.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/diagnose/diagnose.c +[ 11%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentItf.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentItf.cpp:31: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 11%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o -MF CMakeFiles/ngs.dir/NGS_String.c.o.d -o CMakeFiles/ngs.dir/NGS_String.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_String.c -[ 14%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEvent.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 12%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o -MF CMakeFiles/ngs.dir/NGS_Id.c.o.d -o CMakeFiles/ngs.dir/NGS_Id.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Id.c -[ 14%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::PileupItf; C = NGS_Pileup_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 106 | if ( this == 0 ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::PileupItf; C = NGS_Pileup_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 100 | if ( this == 0 ) + | ^~ +[ 12%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o -MF CMakeFiles/ngs.dir/NGS_ErrBlock.c.o.d -o CMakeFiles/ngs.dir/NGS_ErrBlock.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ErrBlock.c +[ 12%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o -MF CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o.d -o CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/FragmentBlobIterator.cpp +[ 12%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o -MF CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o.d -o CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_FragmentBlob.c +[ 12%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupEventItf.cpp +[ 12%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o -MF CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o.d -o CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_FragmentBlobIterator.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupEventItf.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 12%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceBlob.c +[ 12%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupIteratorItf.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupIteratorItf.cpp:30: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 12%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/AlignmentIterator.cpp +[ 12%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupItf.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupItf.cpp:31: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 12%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/AlignmentIterator.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceBlobIterator.c +[ 12%] Building C object libs/ascp/CMakeFiles/ascp.dir/unix/connect.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/sra-sdk-3.0.3+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/ascp/CMakeFiles/ascp.dir/unix/connect.c.o -MF CMakeFiles/ascp.dir/unix/connect.c.o.d -o CMakeFiles/ascp.dir/unix/connect.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c +[ 12%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o -MF CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o.d -o CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/FragmentBlob.cpp +[ 12%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Alignment.cpp +[ 12%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o -MF CMakeFiles/ngs.dir/VByteBlob.c.o.d -o CMakeFiles/ngs.dir/VByteBlob.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/VByteBlob.c +[ 12%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroupIterator.cpp +[ 12%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventIteratorItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, - from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReadCollection.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Alignment.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +/build/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c: In function 'run_ascp': +/build/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c:425:33: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 425 | write(pipeto[1], answer, sizeof y - 1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c:460:49: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 460 | write(pipeto[1], + | ^~~~~~~~~~~~~~~~ + 461 | answer, sizeof y - 1); + | ~~~~~~~~~~~~~~~~~~~~~ In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Read.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroupIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 14%] Building C object libs/loader/CMakeFiles/loader.dir/mmarray.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/mmarray.c.o -MF CMakeFiles/loader.dir/mmarray.c.o.d -o CMakeFiles/loader.dir/mmarray.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/mmarray.c -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 14%] Built target ngs-doc_javadoc -make -f libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build.make libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/DependInfo.cmake --color= -[ 14%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o -MF CMakeFiles/ngs-disp.dir/VTable.cpp.o.d -o CMakeFiles/ngs-disp.dir/VTable.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/VTable.cpp -[ 15%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::PileupEventItf; C = NGS_PileupEvent_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 106 | if ( this == 0 ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::PileupEventItf; C = NGS_PileupEvent_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 100 | if ( this == 0 ) + | ^~ +[ 12%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o -MF CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o.d -o CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ErrBlock.cpp +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o -MF CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/AlignmentItf.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/AlignmentItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/AlignmentItf.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 12%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadIteratorItf.cpp +[ 12%] Linking C static library ../../../ilib/libngs.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cmake -P CMakeFiles/ngs.dir/cmake_clean_target.cmake +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs.dir/link.txt --verbose=1 +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadIteratorItf.cpp:31: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +/usr/bin/ar qc ../../../ilib/libngs.a "CMakeFiles/ngs.dir/NCBI-NGS.c.o" CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o CMakeFiles/ngs.dir/CSRA1_Pileup.c.o CMakeFiles/ngs.dir/CSRA1_Alignment.c.o CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o CMakeFiles/ngs.dir/CSRA1_Reference.c.o CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o CMakeFiles/ngs.dir/CSRA1_Read.c.o CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o CMakeFiles/ngs.dir/SRA_Statistics.c.o CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o CMakeFiles/ngs.dir/SRA_Read.c.o CMakeFiles/ngs.dir/SRA_ReadGroup.c.o CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o CMakeFiles/ngs.dir/SRA_ReadCollection.c.o CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o CMakeFiles/ngs.dir/NGS_Statistics.c.o CMakeFiles/ngs.dir/NGS_ReadCollection.c.o CMakeFiles/ngs.dir/NGS_PileupEvent.c.o CMakeFiles/ngs.dir/NGS_Pileup.c.o CMakeFiles/ngs.dir/NGS_ReadGroup.c.o CMakeFiles/ngs.dir/NGS_Alignment.c.o CMakeFiles/ngs.dir/NGS_Reference.c.o CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o CMakeFiles/ngs.dir/NGS_Read.c.o CMakeFiles/ngs.dir/NGS_Fragment.c.o CMakeFiles/ngs.dir/NGS_Cursor.c.o CMakeFiles/ngs.dir/NGS_Refcount.c.o CMakeFiles/ngs.dir/NGS_String.c.o CMakeFiles/ngs.dir/NGS_Id.c.o CMakeFiles/ngs.dir/NGS_ErrBlock.c.o CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o CMakeFiles/ngs.dir/VByteBlob.c.o +/usr/bin/ranlib ../../../ilib/libngs.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build.make libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build +[ 12%] Built target ngs +make -f libs/general-writer/CMakeFiles/general-writer.dir/build.make libs/general-writer/CMakeFiles/general-writer.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 15%] Building CXX object libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o -[ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o -MF CMakeFiles/ngs.dir/NGS_ErrBlock.c.o.d -o CMakeFiles/ngs.dir/NGS_ErrBlock.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ErrBlock.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o -MF CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o.d -o CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_makedb.cpp -[ 15%] Building C object libs/loader/CMakeFiles/loader.dir/reference-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/reference-writer.c.o -MF CMakeFiles/loader.dir/reference-writer.c.o.d -o CMakeFiles/loader.dir/reference-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/reference-writer.c -[ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/FragmentIterator.cpp -[ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupItf.cpp -[ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o -MF CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o.d -o CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_FragmentBlob.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/general-writer /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/CMakeFiles/general-writer.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f libs/general-writer/CMakeFiles/general-writer.dir/build.make libs/general-writer/CMakeFiles/general-writer.dir/build +[ 12%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadItf.cpp +[ 13%] Building CXX object libs/general-writer/CMakeFiles/general-writer.dir/general-writer.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/general-writer/CMakeFiles/general-writer.dir/general-writer.cpp.o -MF CMakeFiles/general-writer.dir/general-writer.cpp.o.d -o CMakeFiles/general-writer.dir/general-writer.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp +[ 14%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadGroupItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupItf.cpp:31: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadGroupItf.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadItf.cpp:31: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 14%] Building C object libs/general-writer/CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/general-writer/CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o -MF CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o.d -o CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/general-writer/utf8-like-int-codec.c +[ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroup.cpp +[ 15%] Building C object libs/ascp/CMakeFiles/ascp.dir/linux/ascp-path.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/sra-sdk-3.0.3+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/ascp/CMakeFiles/ascp.dir/linux/ascp-path.c.o -MF CMakeFiles/ascp.dir/linux/ascp-path.c.o.d -o CMakeFiles/ascp.dir/linux/ascp-path.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/ascp/linux/ascp-path.c +[ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_FragmentItf.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_FragmentItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | @@ -3029,89 +3025,76 @@ from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/FragmentIterator.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroup.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o -MF CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o.d -o CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_FragmentBlobIterator.c +[ 15%] Linking C static library ../../ilib/libascp.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cmake -P CMakeFiles/ascp.dir/cmake_clean_target.cmake [ 15%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupItf.cpp -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp: In member function 'void ngs::OpaqueRefcount::Release()': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:69:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 69 | if ( this != 0 ) - | ^~ -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp: In member function 'void* ngs::OpaqueRefcount::Duplicate() const': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:100:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] - 100 | if ( this != 0 ) - | ^~ -[ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Fragment.cpp +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cmake -E cmake_link_script CMakeFiles/ascp.dir/link.txt --verbose=1 +/usr/bin/ar qc ../../ilib/libascp.a CMakeFiles/ascp.dir/ascp.c.o CMakeFiles/ascp.dir/unix/connect.c.o "CMakeFiles/ascp.dir/linux/ascp-path.c.o" +/usr/bin/ranlib ../../ilib/libascp.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 15%] Built target ascp +make -f tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 15%] Building CXX object tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o -MF CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o.d -o CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_cpp.cpp +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::AlignmentItf; C = NGS_Alignment_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 106 | if ( this == 0 ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::AlignmentItf; C = NGS_Alignment_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 100 | if ( this == 0 ) + | ^~ In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 15%] Linking CXX static library ../../../ilib/libngs-adapt-c++.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/cmake -P CMakeFiles/ngs-adapt-c++.dir/cmake_clean_target.cmake +[ 15%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupIteratorItf.cpp +[ 15%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReference.cpp +[ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadIterator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Fragment.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReference.hpp:32, + from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReference.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 15%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -MF CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o.d -o CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ErrorMsg.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-adapt-c++.dir/link.txt --verbose=1 -[ 15%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o -/usr/bin/ar qc ../../../ilib/libngs-adapt-c++.a "CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o" -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupIteratorItf.cpp -[ 15%] Building C object libs/loader/CMakeFiles/loader.dir/sequence-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/sequence-writer.c.o -MF CMakeFiles/loader.dir/sequence-writer.c.o.d -o CMakeFiles/loader.dir/sequence-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/sequence-writer.c -/usr/bin/ranlib ../../../ilib/libngs-adapt-c++.a -[ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceBlob.c -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceBlobIterator.c -[ 15%] Built target ngs-adapt-c++ -make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ascp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp/CMakeFiles/ascp.dir/DependInfo.cmake --color= In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadIteratorItf.cpp -[ 15%] Building C object libs/ascp/CMakeFiles/ascp.dir/ascp.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/sra-sdk-3.0.3+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/ascp/CMakeFiles/ascp.dir/ascp.c.o -MF CMakeFiles/ascp.dir/ascp.c.o.d -o CMakeFiles/ascp.dir/ascp.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/ascp/ascp.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadIteratorItf.cpp:31: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 15%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o -MF CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o.d -o CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/FragmentBlobIterator.cpp -[ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadItf.cpp -[ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_FragmentItf.cpp -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadItf.cpp:31: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | [ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_StatisticsItf.cpp -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_FragmentItf.cpp:31: +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | @@ -3120,187 +3103,170 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Statistics.cpp +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReadGroupItf; C = NGS_ReadGroup_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 106 | if ( this == 0 ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReadGroupItf; C = NGS_ReadGroup_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 100 | if ( this == 0 ) + | ^~ +[ 15%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReadItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReadItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadItf.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadItf.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | [ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Package.cpp -[ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o -MF CMakeFiles/ngs.dir/VByteBlob.c.o.d -o CMakeFiles/ngs.dir/VByteBlob.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/VByteBlob.c -[ 15%] Linking C static library ../../ilib/libloader.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cmake -P CMakeFiles/loader.dir/cmake_clean_target.cmake +[ 15%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadCollectionItf.cpp +[ 16%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_String.cpp +[ 16%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Refcount.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Statistics.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Statistics.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_String.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/StringRef.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/loader.dir/link.txt --verbose=1 -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Package.cpp:31: +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Refcount.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -/usr/bin/ar qc ../../ilib/libloader.a CMakeFiles/loader.dir/progressbar.c.o "CMakeFiles/loader.dir/loader-file.c.o" "CMakeFiles/loader.dir/loader-meta.c.o" "CMakeFiles/loader.dir/queue-file.c.o" "CMakeFiles/loader.dir/alignment-writer.c.o" "CMakeFiles/loader.dir/common-reader.c.o" "CMakeFiles/loader.dir/common-writer.c.o" CMakeFiles/loader.dir/mmarray.c.o "CMakeFiles/loader.dir/reference-writer.c.o" "CMakeFiles/loader.dir/sequence-writer.c.o" -[ 15%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadCollectionItf.cpp -/usr/bin/ranlib ../../ilib/libloader.a -[ 15%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupItf.cpp -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 15%] Built target loader -make -f libs/diagnose/CMakeFiles/diagnose.dir/build.make libs/diagnose/CMakeFiles/diagnose.dir/depend -[ 15%] Linking CXX static library ../../../ilib/libngs-disp.a -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/diagnose /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose/CMakeFiles/diagnose.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/cmake -P CMakeFiles/ngs-disp.dir/cmake_clean_target.cmake In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/StringRef.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Package.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-disp.dir/link.txt --verbose=1 In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadCollectionItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadCollectionItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/diagnose/CMakeFiles/diagnose.dir/build.make libs/diagnose/CMakeFiles/diagnose.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 15%] Linking C static library ../../../ilib/libngs.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cmake -P CMakeFiles/ngs.dir/cmake_clean_target.cmake -/usr/bin/ar qc ../../../ilib/libngs-disp.a "CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "CMakeFiles/ngs-disp.dir/VTable.cpp.o" "CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" -[ 15%] Building C object libs/ascp/CMakeFiles/ascp.dir/unix/connect.c.o +[ 16%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/sra-sdk-3.0.3+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/ascp/CMakeFiles/ascp.dir/unix/connect.c.o -MF CMakeFiles/ascp.dir/unix/connect.c.o.d -o CMakeFiles/ascp.dir/unix/connect.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c -[ 15%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/sra-sdk-3.0.3+dfsg/libs/diagnose -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o -MF CMakeFiles/diagnose.dir/diagnose.c.o.d -o CMakeFiles/diagnose.dir/diagnose.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/diagnose/diagnose.c -/usr/bin/ranlib ../../../ilib/libngs-disp.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs.dir/link.txt --verbose=1 -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 15%] Built target ngs-disp -/usr/bin/ar qc ../../../ilib/libngs.a "CMakeFiles/ngs.dir/NCBI-NGS.c.o" CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o CMakeFiles/ngs.dir/CSRA1_Pileup.c.o CMakeFiles/ngs.dir/CSRA1_Alignment.c.o CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o CMakeFiles/ngs.dir/CSRA1_Reference.c.o CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o CMakeFiles/ngs.dir/CSRA1_Read.c.o CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o CMakeFiles/ngs.dir/SRA_Statistics.c.o CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o CMakeFiles/ngs.dir/SRA_Read.c.o CMakeFiles/ngs.dir/SRA_ReadGroup.c.o CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o CMakeFiles/ngs.dir/SRA_ReadCollection.c.o CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o CMakeFiles/ngs.dir/NGS_Statistics.c.o CMakeFiles/ngs.dir/NGS_ReadCollection.c.o CMakeFiles/ngs.dir/NGS_PileupEvent.c.o CMakeFiles/ngs.dir/NGS_Pileup.c.o CMakeFiles/ngs.dir/NGS_ReadGroup.c.o CMakeFiles/ngs.dir/NGS_Alignment.c.o CMakeFiles/ngs.dir/NGS_Reference.c.o CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o CMakeFiles/ngs.dir/NGS_Read.c.o CMakeFiles/ngs.dir/NGS_Fragment.c.o CMakeFiles/ngs.dir/NGS_Cursor.c.o CMakeFiles/ngs.dir/NGS_Refcount.c.o CMakeFiles/ngs.dir/NGS_String.c.o CMakeFiles/ngs.dir/NGS_Id.c.o CMakeFiles/ngs.dir/NGS_ErrBlock.c.o CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o CMakeFiles/ngs.dir/VByteBlob.c.o -make -f libs/general-writer/CMakeFiles/general-writer.dir/build.make libs/general-writer/CMakeFiles/general-writer.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/general-writer /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/CMakeFiles/general-writer.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/general-writer/CMakeFiles/general-writer.dir/build.make libs/general-writer/CMakeFiles/general-writer.dir/build -/usr/bin/ranlib ../../../ilib/libngs.a -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 15%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o -MF CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o.d -o CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/FragmentBlob.cpp -/build/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c: In function 'run_ascp': -/build/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c:425:33: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 425 | write(pipeto[1], answer, sizeof y - 1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c:460:49: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 460 | write(pipeto[1], - | ^~~~~~~~~~~~~~~~ - 461 | answer, sizeof y - 1); - | ~~~~~~~~~~~~~~~~~~~~~ -[ 16%] Building CXX object libs/general-writer/CMakeFiles/general-writer.dir/general-writer.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/general-writer/CMakeFiles/general-writer.dir/general-writer.cpp.o -MF CMakeFiles/general-writer.dir/general-writer.cpp.o.d -o CMakeFiles/general-writer.dir/general-writer.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 16%] Built target ngs -make -f tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/DependInfo.cmake --color= -[ 17%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_String.cpp -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_String.cpp:30: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 17%] Building CXX object tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o -MF CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o.d -o CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_cpp.cpp -[ 17%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Refcount.cpp -[ 17%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Refcount.cpp:30: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ErrorMsg.cpp -[ 17%] Building C object libs/general-writer/CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/general-writer/CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o -MF CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o.d -o CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/general-writer/utf8-like-int-codec.c -[ 17%] Building C object libs/ascp/CMakeFiles/ascp.dir/linux/ascp-path.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/sra-sdk-3.0.3+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/ascp/CMakeFiles/ascp.dir/linux/ascp-path.c.o -MF CMakeFiles/ascp.dir/linux/ascp-path.c.o.d -o CMakeFiles/ascp.dir/linux/ascp-path.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/ascp/linux/ascp-path.c -[ 17%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReference.cpp -[ 17%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o -MF CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o.d -o CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/ReferenceBlob.cpp -[ 17%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupIteratorItf.cpp -[ 18%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadItf.cpp -[ 18%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o -MF CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o.d -o CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/ReferenceBlobIterator.cpp -[ 18%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadIteratorItf.cpp +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReadItf; C = NGS_Read_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 106 | if ( this == 0 ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReadItf; C = NGS_Read_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 100 | if ( this == 0 ) + | ^~ +[ 16%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Read.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Read.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Read.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReference.hpp:32, - from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReference.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Read.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 18%] Linking C static library ../../ilib/libascp.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cmake -P CMakeFiles/ascp.dir/cmake_clean_target.cmake -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupIteratorItf.cpp:30: +[ 16%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o +[ 16%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ErrorMsg.cpp +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o -MF CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o.d -o CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/ReferenceBlob.cpp +/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = short unsigned int; uint8_t = unsigned char]': +/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:646:17: warning: unused variable 'ret2' [-Wunused-variable] + 646 | int ret2 = decode_uint16 ( start, start + ret, & val2 ); + | ^~~~ +/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = unsigned int; uint8_t = unsigned char]': +/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:659:17: warning: unused variable 'ret2' [-Wunused-variable] + 659 | int ret2 = decode_uint32 ( start, start + ret, & val2 ); + | ^~~~ +/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = long unsigned int; uint8_t = unsigned char]': +/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:672:17: warning: unused variable 'ret2' [-Wunused-variable] + 672 | int ret2 = decode_uint64 ( start, start + ret, & val2 ); + | ^~~~ +[ 16%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o -MF CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/FragmentItf.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/FragmentItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 18%] Linking CXX static library ../../../../ilib/libngs-bind-c++.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cmake -E cmake_link_script CMakeFiles/ascp.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/cmake -P CMakeFiles/ngs-bind-c++.dir/cmake_clean_target.cmake -/usr/bin/ar qc ../../ilib/libascp.a CMakeFiles/ascp.dir/ascp.c.o CMakeFiles/ascp.dir/unix/connect.c.o "CMakeFiles/ascp.dir/linux/ascp-path.c.o" -[ 19%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbAlignment.cpp -/usr/bin/ranlib ../../ilib/libascp.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-c++.dir/link.txt --verbose=1 -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadItf.cpp:30: +[ 16%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o -MF CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StatisticsItf.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StatisticsItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StatisticsItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadIteratorItf.cpp:30: +[ 16%] Linking CXX executable ../../../test-bin/ngs-makedb +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-makedb.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o" -o ../../../test-bin/ngs-makedb -Wl,-Bstatic -lktst -lkapp -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +[ 16%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/FragmentIterator.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/FragmentIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +[ 16%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o -MF CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o.d -o CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/ReferenceBlobIterator.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/usr/bin/ar qc ../../../../ilib/libngs-bind-c++.a "CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" -[ 19%] Built target ascp +[ 16%] Built target ngs-makedb make -f tools/external/vdb-config/tui/CMakeFiles/tui.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui/CMakeFiles/tui.dir/DependInfo.cmake --color= -/usr/bin/ranlib ../../../../ilib/libngs-bind-c++.a +[ 16%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Fragment.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-config/tui/CMakeFiles/tui.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui.dir/build -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 16%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PackageItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PackageItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PackageItf.cpp +[ 17%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbAlignment.cpp +[ 17%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/dir_dlg.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/dir_dlg.c.o -MF CMakeFiles/tui.dir/dir_dlg.c.o.d -o CMakeFiles/tui.dir/dir_dlg.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/dir_dlg.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Fragment.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 17%] Linking CXX static library ../../../../ilib/libtui_cpp.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -P CMakeFiles/tui_cpp.dir/cmake_clean_target.cmake +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -E cmake_link_script CMakeFiles/tui_cpp.dir/link.txt --verbose=1 +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::FragmentItf; C = NGS_Fragment_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 106 | if ( this == 0 ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::FragmentItf; C = NGS_Fragment_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 100 | if ( this == 0 ) + | ^~ +[ 17%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Statistics.cpp +/usr/bin/ar qc ../../../../ilib/libtui_cpp.a CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PackageItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PackageItf.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +/usr/bin/ranlib ../../../../ilib/libtui_cpp.a In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -3311,63 +3277,100 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/dir_dlg.c.o -[ 19%] Built target ngs-bind-c++ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/dir_dlg.c.o -MF CMakeFiles/tui.dir/dir_dlg.c.o.d -o CMakeFiles/tui.dir/dir_dlg.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/dir_dlg.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 17%] Built target tui_cpp make -f tools/external/sra-dump/CMakeFiles/fastq-dump.dir/build.make tools/external/sra-dump/CMakeFiles/fastq-dump.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/fastq-dump.dir/DependInfo.cmake --color= -make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/sff-dump.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-dump/CMakeFiles/fastq-dump.dir/build.make tools/external/sra-dump/CMakeFiles/fastq-dump.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 19%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/factory.c.o +[ 17%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/factory.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/factory.c.o -MF CMakeFiles/fastq-dump.dir/factory.c.o.d -o CMakeFiles/fastq-dump.dir/factory.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c -[ 19%] Linking CXX static library ../../../../ilib/libngs-bind-java.a +[ 17%] Linking CXX static library ../../../../ilib/libngs-bind-java.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/cmake -P CMakeFiles/ngs-bind-java.dir/cmake_clean_target.cmake -[ 19%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/factory.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/factory.c.o -MF CMakeFiles/sff-dump.dir/factory.c.o.d -o CMakeFiles/sff-dump.dir/factory.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c +[ 17%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupIteratorItf.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-java.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../ilib/libngs-bind-java.a "CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o" /usr/bin/ranlib ../../../../ilib/libngs-bind-java.a +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Statistics.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Statistics.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::StatisticsItf; C = NGS_Statistics_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 106 | if ( this == 0 ) + | ^~ +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupIteratorItf.cpp:30: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 17%] Built target ngs-bind-java +make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/sff-dump.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 19%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o +make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 17%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/factory.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/factory.c.o -MF CMakeFiles/sff-dump.dir/factory.c.o.d -o CMakeFiles/sff-dump.dir/factory.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c +[ 17%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/eventring.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/eventring.c.o -MF CMakeFiles/tui.dir/eventring.c.o.d -o CMakeFiles/tui.dir/eventring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/eventring.c +/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c: In function 'sqlite3DefaultRowEst': +/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102377:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] +102377 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) ); + | ^~ +[ 17%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o -MF CMakeFiles/ngs-disp.dir/StringItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/StringItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:11540: +/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102377:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' +102377 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) ); + | ^~~~~~ +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 17%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o -MF CMakeFiles/ngs-disp.dir/Refcount.cpp.o.d -o CMakeFiles/ngs-disp.dir/Refcount.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp +/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102378:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] +102378 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) ); + | ^~ +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102378:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' +102378 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) ); + | ^~~~~~ +[ 17%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/file_dlg.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/file_dlg.c.o -MF CMakeFiles/tui.dir/file_dlg.c.o.d -o CMakeFiles/tui.dir/file_dlg.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/file_dlg.c +[ 17%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/StringRef.cpp +[ 17%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o -MF CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o.d -o CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/NGS-VDB.cpp -[ 19%] Linking CXX executable ../../../test-bin/ngs-makedb -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-makedb.dir/link.txt --verbose=1 -[ 19%] Built target ngs-bind-java make -f tools/external/sra-dump/CMakeFiles/illumina-dump.dir/build.make tools/external/sra-dump/CMakeFiles/illumina-dump.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/illumina-dump.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o" -o ../../../test-bin/ngs-makedb -Wl,-Bstatic -lktst -lkapp -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-dump/CMakeFiles/illumina-dump.dir/build.make tools/external/sra-dump/CMakeFiles/illumina-dump.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceItf.cpp -[ 19%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/factory.c.o +[ 17%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/factory.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/factory.c.o -MF CMakeFiles/illumina-dump.dir/factory.c.o.d -o CMakeFiles/illumina-dump.dir/factory.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c -[ 19%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o -[ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/vdb-sqlite\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o -MF CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o.d -o CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3vdb.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceIteratorItf.cpp -/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = short unsigned int; uint8_t = unsigned char]': -/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:646:17: warning: unused variable 'ret2' [-Wunused-variable] - 646 | int ret2 = decode_uint16 ( start, start + ret, & val2 ); - | ^~~~ -/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = unsigned int; uint8_t = unsigned char]': -/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:659:17: warning: unused variable 'ret2' [-Wunused-variable] - 659 | int ret2 = decode_uint32 ( start, start + ret, & val2 ); - | ^~~~ -/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = long unsigned int; uint8_t = unsigned char]': -/build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:672:17: warning: unused variable 'ret2' [-Wunused-variable] - 672 | int ret2 = decode_uint64 ( start, start + ret, & val2 ); - | ^~~~ +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/StringRef.cpp:27: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -3384,205 +3387,184 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/eventring.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/eventring.c.o -MF CMakeFiles/tui.dir/eventring.c.o.d -o CMakeFiles/tui.dir/eventring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/eventring.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceItf.cpp:30: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceIteratorItf.cpp:30: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceSequenceItf.cpp -[ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StatisticsItf.cpp -[ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/file_dlg.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/file_dlg.c.o -MF CMakeFiles/tui.dir/file_dlg.c.o.d -o CMakeFiles/tui.dir/file_dlg.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/file_dlg.c -[ 19%] Linking CXX static library ../../../../ilib/libtui_cpp.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -P CMakeFiles/tui_cpp.dir/cmake_clean_target.cmake -/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c: In function 'sqlite3DefaultRowEst': -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StatisticsItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StatisticsItf.cpp:30: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -E cmake_link_script CMakeFiles/tui_cpp.dir/link.txt --verbose=1 -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceSequenceItf.cpp:30: +[ 18%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadItf.cpp +[ 18%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/endpoint.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/sra-sdk-3.0.3+dfsg/libs/diagnose -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/diagnose/CMakeFiles/diagnose.dir/endpoint.c.o -MF CMakeFiles/diagnose.dir/endpoint.c.o.d -o CMakeFiles/diagnose.dir/endpoint.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/diagnose/endpoint.c +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp: In member function 'void ngs::OpaqueRefcount::Release()': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:69:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 69 | if ( this != 0 ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp: In member function 'void* ngs::OpaqueRefcount::Duplicate() const': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:100:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 100 | if ( this != 0 ) + | ^~ +[ 18%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o -MF CMakeFiles/ngs-disp.dir/VTable.cpp.o.d -o CMakeFiles/ngs-disp.dir/VTable.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/VTable.cpp +[ 18%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/vdb-sqlite\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o -MF CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o.d -o CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3vdb.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102377:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] -102377 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) ); - | ^~ -[ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o -/usr/bin/ar qc ../../../../ilib/libtui_cpp.a CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_Refcount.cpp -/usr/bin/ranlib ../../../../ilib/libtui_cpp.a -In file included from /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:11540: -/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102377:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' -102377 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) ); - | ^~~~~~ -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 19%] Built target ngs-makedb +[ 18%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/line_policy.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/line_policy.c.o -MF CMakeFiles/tui.dir/line_policy.c.o.d -o CMakeFiles/tui.dir/line_policy.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/line_policy.c +[ 18%] Linking C static library ../../ilib/libdiagnose.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cmake -P CMakeFiles/diagnose.dir/cmake_clean_target.cmake +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cmake -E cmake_link_script CMakeFiles/diagnose.dir/link.txt --verbose=1 +[ 19%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o -MF CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o.d -o CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ErrBlock.cpp make -f tools/external/sra-dump/CMakeFiles/abi-dump.dir/build.make tools/external/sra-dump/CMakeFiles/abi-dump.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/abi-dump.dir/DependInfo.cmake --color= -/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102378:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] -102378 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) ); - | ^~ -[ 19%] Built target tui_cpp -make -f tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build.make tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/DependInfo.cmake --color= +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp: In member function 'const char* ngs::StringItf::data() const': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:62:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 62 | if ( this != 0 ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp: In member function 'size_t ngs::StringItf::size() const': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:97:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 97 | if ( this != 0 ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::StringItf; C = NGS_String_v1]': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] + 106 | if ( this == 0 ) + | ^~ +/usr/bin/ar qc ../../ilib/libdiagnose.a CMakeFiles/diagnose.dir/diagnose.c.o CMakeFiles/diagnose.dir/endpoint.c.o +/usr/bin/ranlib ../../ilib/libdiagnose.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102378:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' -102378 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) ); - | ^~~~~~ make -f tools/external/sra-dump/CMakeFiles/abi-dump.dir/build.make tools/external/sra-dump/CMakeFiles/abi-dump.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build.make tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build +[ 19%] Built target diagnose +make -f tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build.make tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/DependInfo.cmake --color= [ 19%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/factory.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/factory.c.o -MF CMakeFiles/abi-dump.dir/factory.c.o.d -o CMakeFiles/abi-dump.dir/factory.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build.make tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 19%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/dyn_string.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/dyn_string.c.o -MF CMakeFiles/sra-pileup.dir/dyn_string.c.o.d -o CMakeFiles/sra-pileup.dir/dyn_string.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/dyn_string.c -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_Refcount.cpp:30: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -[ 19%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/fasta_dump.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/fasta_dump.c.o -MF CMakeFiles/sff-dump.dir/fasta_dump.c.o.d -o CMakeFiles/sff-dump.dir/fasta_dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c -[ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/line_policy.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/line_policy.c.o -MF CMakeFiles/tui.dir/line_policy.c.o.d -o CMakeFiles/tui.dir/line_policy.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/line_policy.c -[ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StringItf.cpp -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StringItf.cpp:30: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | +[ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/screen.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/screen.c.o -MF CMakeFiles/tui.dir/screen.c.o.d -o CMakeFiles/tui.dir/screen.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/screen.c [ 20%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fasta_dump.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fasta_dump.c.o -MF CMakeFiles/fastq-dump.dir/fasta_dump.c.o.d -o CMakeFiles/fastq-dump.dir/fasta_dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c -[ 20%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/fasta_dump.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/fasta_dump.c.o -MF CMakeFiles/illumina-dump.dir/fasta_dump.c.o.d -o CMakeFiles/illumina-dump.dir/fasta_dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c [ 20%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o -MF CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o.d -o CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c -[ 20%] Linking CXX static library ../../ilib/libngs-vdb.a +[ 20%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -MF CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o.d -o CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ErrorMsg.cpp +[ 21%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/string_cache.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/string_cache.c.o -MF CMakeFiles/tui.dir/string_cache.c.o.d -o CMakeFiles/tui.dir/string_cache.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/string_cache.c +[ 21%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/fasta_dump.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/fasta_dump.c.o -MF CMakeFiles/sff-dump.dir/fasta_dump.c.o.d -o CMakeFiles/sff-dump.dir/fasta_dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c +[ 21%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/fasta_dump.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/fasta_dump.c.o -MF CMakeFiles/illumina-dump.dir/fasta_dump.c.o.d -o CMakeFiles/illumina-dump.dir/fasta_dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c: In function 'foreach_argument': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c:443:20: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] + 443 | if ( rc == 0 && path != NULL ) { + | ^ +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c:394:10: note: 'rc' was declared here + 394 | rc_t rc; + | ^~ +[ 22%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/core.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/core.c.o -MF CMakeFiles/sff-dump.dir/core.c.o.d -o CMakeFiles/sff-dump.dir/core.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c +[ 22%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/core.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/core.c.o -MF CMakeFiles/fastq-dump.dir/core.c.o.d -o CMakeFiles/fastq-dump.dir/core.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 1010 | ReportBuildDate ( __DATE__ ); + | ^~~~~~~~ +[ 22%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui.c.o -MF CMakeFiles/tui.dir/tui.c.o.d -o CMakeFiles/tui.dir/tui.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui.c +[ 22%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/out_redir.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/out_redir.c.o -MF CMakeFiles/sra-pileup.dir/out_redir.c.o.d -o CMakeFiles/sra-pileup.dir/out_redir.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/out_redir.c +[ 22%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg.c.o -MF CMakeFiles/tui.dir/tui_dlg.c.o.d -o CMakeFiles/tui.dir/tui_dlg.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_dlg.c +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 1010 | ReportBuildDate ( __DATE__ ); + | ^~~~~~~~ +[ 22%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadIteratorItf.cpp +[ 22%] Linking CXX static library ../../ilib/libngs-vdb.a +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadIteratorItf.cpp:30: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/cmake -P CMakeFiles/ngs-vdb.dir/cmake_clean_target.cmake cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-vdb.dir/link.txt --verbose=1 -[ 21%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/core.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/core.c.o -MF CMakeFiles/sff-dump.dir/core.c.o.d -o CMakeFiles/sff-dump.dir/core.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c +[ 22%] Linking CXX static library ../../../../ilib/libngs-bind-c++.a +[ 22%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/sff.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/sff.c.o -MF CMakeFiles/sff-dump.dir/sff.c.o.d -o CMakeFiles/sff-dump.dir/sff.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/sff.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/cmake -P CMakeFiles/ngs-bind-c++.dir/cmake_clean_target.cmake /usr/bin/ar qc ../../ilib/libngs-vdb.a "CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o" "CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o" "CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o" "CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o" "CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o" "CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o" "CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o" "CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o" -[ 21%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/screen.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/screen.c.o -MF CMakeFiles/tui.dir/screen.c.o.d -o CMakeFiles/tui.dir/screen.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/screen.c /usr/bin/ranlib ../../ilib/libngs-vdb.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 21%] Built target ngs-vdb +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-c++.dir/link.txt --verbose=1 +[ 22%] Built target ngs-vdb make -f tools/external/sra-pileup/CMakeFiles/sam-dump.dir/build.make tools/external/sra-pileup/CMakeFiles/sam-dump.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup/CMakeFiles/sam-dump.dir/DependInfo.cmake --color= +/usr/bin/ar qc ../../../../ilib/libngs-bind-c++.a "CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" +[ 22%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/perf_log.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/perf_log.c.o -MF CMakeFiles/sra-pileup.dir/perf_log.c.o.d -o CMakeFiles/sra-pileup.dir/perf_log.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/perf_log.c +/usr/bin/ranlib ../../../../ilib/libngs-bind-c++.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-pileup/CMakeFiles/sam-dump.dir/build.make tools/external/sra-pileup/CMakeFiles/sam-dump.dir/build +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 21%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/fasta_dump.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/fasta_dump.c.o -MF CMakeFiles/abi-dump.dir/fasta_dump.c.o.d -o CMakeFiles/abi-dump.dir/fasta_dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c +[ 22%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/inputfiles.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/inputfiles.c.o -MF CMakeFiles/sam-dump.dir/inputfiles.c.o.d -o CMakeFiles/sam-dump.dir/inputfiles.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/inputfiles.c +[ 22%] Built target ngs-bind-c++ make -f tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build.make tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/DependInfo.cmake --color= -[ 21%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/inputfiles.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/inputfiles.c.o -MF CMakeFiles/sam-dump.dir/inputfiles.c.o.d -o CMakeFiles/sam-dump.dir/inputfiles.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/inputfiles.c -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 1010 | ReportBuildDate ( __DATE__ ); - | ^~~~~~~~ +[ 22%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/core.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/core.c.o -MF CMakeFiles/illumina-dump.dir/core.c.o.d -o CMakeFiles/illumina-dump.dir/core.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build.make tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 21%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/core.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/core.c.o -MF CMakeFiles/illumina-dump.dir/core.c.o.d -o CMakeFiles/illumina-dump.dir/core.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c -[ 22%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/helper.c.o -[ 22%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/perf_log.c.o +[ 22%] Linking CXX static library ../../../ilib/libngs-disp.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/cmake -P CMakeFiles/ngs-disp.dir/cmake_clean_target.cmake +[ 23%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/helper.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/helper.c.o -MF CMakeFiles/fasterq-dump.dir/helper.c.o.d -o CMakeFiles/fasterq-dump.dir/helper.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/helper.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/perf_log.c.o -MF CMakeFiles/sam-dump.dir/perf_log.c.o.d -o CMakeFiles/sam-dump.dir/perf_log.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/perf_log.c -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c: In function 'foreach_argument': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c:443:20: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] - 443 | if ( rc == 0 && path != NULL ) { - | ^ -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c:394:10: note: 'rc' was declared here - 394 | rc_t rc; - | ^~ -[ 23%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/rna_splice_log.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic 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-I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o -MF CMakeFiles/fasterq-dump.dir/arg_helper.c.o.d -o CMakeFiles/fasterq-dump.dir/arg_helper.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/arg_helper.c -[ 23%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/core.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/core.c.o -MF CMakeFiles/fastq-dump.dir/core.c.o.d -o CMakeFiles/fastq-dump.dir/core.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c -[ 24%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/string_cache.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/string_cache.c.o -MF CMakeFiles/tui.dir/string_cache.c.o.d -o CMakeFiles/tui.dir/string_cache.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/string_cache.c -[ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/out_redir.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/out_redir.c.o -MF CMakeFiles/sra-pileup.dir/out_redir.c.o.d -o CMakeFiles/sra-pileup.dir/out_redir.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/out_redir.c -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 1010 | ReportBuildDate ( __DATE__ ); - | ^~~~~~~~ -[ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump-opts.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump-opts.c.o -MF CMakeFiles/sam-dump.dir/sam-dump-opts.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump-opts.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump-opts.c -[ 24%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/core.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/core.c.o -MF CMakeFiles/abi-dump.dir/core.c.o.d -o CMakeFiles/abi-dump.dir/core.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c -[ 24%] Linking CXX static library ../../../../ilib/libngs-bind-python.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/cmake -P CMakeFiles/ngs-bind-python.dir/cmake_clean_target.cmake -[ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/out_redir.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/out_redir.c.o -MF CMakeFiles/sam-dump.dir/out_redir.c.o.d -o CMakeFiles/sam-dump.dir/out_redir.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/out_redir.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-python.dir/link.txt --verbose=1 -[ 24%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG 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"CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o" -[ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr.c.o -MF CMakeFiles/sam-dump.dir/sam-hdr.c.o.d -o CMakeFiles/sam-dump.dir/sam-hdr.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-hdr.c -/usr/bin/ranlib ../../../../ilib/libngs-bind-python.a -[ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/perf_log.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/perf_log.c.o -MF CMakeFiles/sra-pileup.dir/perf_log.c.o.d -o CMakeFiles/sra-pileup.dir/perf_log.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/perf_log.c -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 1010 | ReportBuildDate ( __DATE__ ); - | ^~~~~~~~ -[ 25%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/abi.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/abi.c.o -MF CMakeFiles/abi-dump.dir/abi.c.o.d -o 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+/usr/bin/ranlib ../../../ilib/libngs-disp.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 25%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui.c.o -MF CMakeFiles/tui.dir/tui.c.o.d -o CMakeFiles/tui.dir/tui.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui.c -[ 25%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o -MF CMakeFiles/fasterq-dump.dir/tool_ctx.c.o.d -o CMakeFiles/fasterq-dump.dir/tool_ctx.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/tool_ctx.c -[ 25%] Built target ngs-bind-python +[ 23%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg_helper.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg_helper.c.o -MF CMakeFiles/tui.dir/tui_dlg_helper.c.o.d -o CMakeFiles/tui.dir/tui_dlg_helper.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_dlg_helper.c +[ 23%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/reref.c.o +[ 23%] Built target ngs-disp +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/reref.c.o -MF CMakeFiles/sra-pileup.dir/reref.c.o.d -o CMakeFiles/sra-pileup.dir/reref.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c make -f tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/build.make tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/depend +[ 23%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/DependInfo.cmake --color= -[ 25%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/inspector.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/inspector.c.o -MF CMakeFiles/fasterq-dump.dir/inspector.c.o.d -o CMakeFiles/fasterq-dump.dir/inspector.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/inspector.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceItf.cpp +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 1010 | ReportBuildDate ( __DATE__ ); + | ^~~~~~~~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/build.make tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr1.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr1.c.o -MF CMakeFiles/sam-dump.dir/sam-hdr1.c.o.d -o CMakeFiles/sam-dump.dir/sam-hdr1.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-hdr1.c -[ 25%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o +[ 23%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 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tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/reref.c.o -MF CMakeFiles/sra-pileup.dir/reref.c.o.d -o CMakeFiles/sra-pileup.dir/reref.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c -[ 25%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg.c.o -MF CMakeFiles/tui.dir/tui_dlg.c.o.d -o CMakeFiles/tui.dir/tui_dlg.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_dlg.c -[ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/matecache.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/matecache.c.o -MF CMakeFiles/sam-dump.dir/matecache.c.o.d -o CMakeFiles/sam-dump.dir/matecache.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/matecache.c +[ 24%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-coldefs.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceItf.cpp:30: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 24%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/fasta_dump.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/fasta_dump.c.o -MF CMakeFiles/abi-dump.dir/fasta_dump.c.o.d -o CMakeFiles/abi-dump.dir/fasta_dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c +[ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/perf_log.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/perf_log.c.o -MF CMakeFiles/sam-dump.dir/perf_log.c.o.d -o CMakeFiles/sam-dump.dir/perf_log.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/perf_log.c In function 'report_ref_table2', inlined from 'report_ref_obj' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:367:14, inlined from 'report_ref_database' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:408:34, @@ -3619,106 +3601,37 @@ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:137:21: note: 'max_prim_at' was declared here 137 | int64_t row_id, max_prim_at, max_sec_at, max_ev_at; | ^~~~~~~~~~~ -[ 25%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sbuffer.c.o -cd 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/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_menu.c.o -MF CMakeFiles/tui.dir/tui_menu.c.o.d -o CMakeFiles/tui.dir/tui_menu.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c +[ 24%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o -MF CMakeFiles/fasterq-dump.dir/arg_helper.c.o.d -o CMakeFiles/fasterq-dump.dir/arg_helper.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/arg_helper.c +[ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/rna_splice_log.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/rna_splice_log.c.o -MF CMakeFiles/sam-dump.dir/rna_splice_log.c.o.d -o CMakeFiles/sam-dump.dir/rna_splice_log.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/rna_splice_log.c [ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cg_tools.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cg_tools.c.o -MF CMakeFiles/sra-pileup.dir/cg_tools.c.o.d -o CMakeFiles/sra-pileup.dir/cg_tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c -[ 25%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/endpoint.c.o -[ 26%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/sra-sdk-3.0.3+dfsg/libs/diagnose -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/diagnose/CMakeFiles/diagnose.dir/endpoint.c.o -MF CMakeFiles/diagnose.dir/endpoint.c.o.d -o CMakeFiles/diagnose.dir/endpoint.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/diagnose/endpoint.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-coldefs.c +[ 25%] Linking CXX static library ../../ilib/libgeneral-writer.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -P CMakeFiles/general-writer.dir/cmake_clean_target.cmake +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -E cmake_link_script CMakeFiles/general-writer.dir/link.txt --verbose=1 +/usr/bin/ar qc ../../ilib/libgeneral-writer.a "CMakeFiles/general-writer.dir/general-writer.cpp.o" "CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o" +/usr/bin/ranlib ../../ilib/libgeneral-writer.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'fmt_cigar_elem': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:491:10: warning: unused variable 'rc' [-Wunused-variable] 491 | rc_t rc = string_printf ( dst, 11, &num_writ, "%d%c", cig_oplen, cig_op ); | ^~ -[ 26%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/err_msg.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb 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-I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fastq.c.o -MF CMakeFiles/fastq-dump.dir/fastq.c.o.d -o CMakeFiles/fastq-dump.dir/fastq.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fastq.c -[ 26%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/read_fkt.c.o -[ 26%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-aligned.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 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-ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg_helper.c.o -MF CMakeFiles/tui.dir/tui_dlg_helper.c.o.d -o CMakeFiles/tui.dir/tui_dlg_helper.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_dlg_helper.c -[ 26%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_tools.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_tools.c.o -MF CMakeFiles/fasterq-dump.dir/file_tools.c.o.d -o CMakeFiles/fasterq-dump.dir/file_tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/file_tools.c -[ 26%] Linking C static library ../../ilib/libdiagnose.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cmake -P CMakeFiles/diagnose.dir/cmake_clean_target.cmake -[ 27%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-unaligned.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-unaligned.c.o -MF CMakeFiles/sam-dump.dir/sam-unaligned.c.o.d -o CMakeFiles/sam-dump.dir/sam-unaligned.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c -[ 27%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/sff.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cmake -E cmake_link_script CMakeFiles/diagnose.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/sff.c.o -MF CMakeFiles/sff-dump.dir/sff.c.o.d -o CMakeFiles/sff-dump.dir/sff.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/sff.c -[ 27%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/md_flag.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/md_flag.c.o -MF CMakeFiles/sam-dump.dir/md_flag.c.o.d -o CMakeFiles/sam-dump.dir/md_flag.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/md_flag.c -/usr/bin/ar qc ../../ilib/libdiagnose.a CMakeFiles/diagnose.dir/diagnose.c.o CMakeFiles/diagnose.dir/endpoint.c.o -/usr/bin/ranlib ../../ilib/libdiagnose.a -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 27%] Built target diagnose +[ 25%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o -MF CMakeFiles/fasterq-dump.dir/dflt_defline.c.o.d -o CMakeFiles/fasterq-dump.dir/dflt_defline.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/dflt_defline.c +[ 25%] Built target general-writer make -f tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/build.make tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/build.make tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 27%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/illumina.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/illumina.c.o -MF CMakeFiles/illumina-dump.dir/illumina.c.o.d -o CMakeFiles/illumina-dump.dir/illumina.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/illumina.c -[ 27%] Building C object tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/vdb-validate.c.o +[ 25%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/core.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/core.c.o -MF CMakeFiles/abi-dump.dir/core.c.o.d -o CMakeFiles/abi-dump.dir/core.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c +[ 25%] Building C object tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/vdb-validate.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-validate\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/vdb-validate.c.o -MF CMakeFiles/vdb-validate.dir/vdb-validate.c.o.d -o CMakeFiles/vdb-validate.dir/vdb-validate.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c -[ 27%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_menu.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_menu.c.o -MF CMakeFiles/tui.dir/tui_menu.c.o.d -o CMakeFiles/tui.dir/tui_menu.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c: In function 'print_sliced_quality': -[ 27%] Linking C executable ../../../bin/sff-dump -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c:407:12: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] - 407 | return rc; - | ^~ -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c:391:10: note: 'rc' was declared here - 391 | rc_t rc; - | ^~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/sff-dump.dir/link.txt --verbose=1 -[ 27%] Linking C executable ../../../bin/abi-dump -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/abi-dump.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sff-dump.dir/factory.c.o" "CMakeFiles/sff-dump.dir/fasta_dump.c.o" "CMakeFiles/sff-dump.dir/core.c.o" "CMakeFiles/sff-dump.dir/sff.c.o" -o ../../../bin/sff-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 27%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/cg_tools.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/cg_tools.c.o -MF CMakeFiles/sam-dump.dir/cg_tools.c.o.d -o CMakeFiles/sam-dump.dir/cg_tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/abi-dump.dir/factory.c.o" "CMakeFiles/abi-dump.dir/fasta_dump.c.o" "CMakeFiles/abi-dump.dir/core.c.o" "CMakeFiles/abi-dump.dir/abi.c.o" -o ../../../bin/abi-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 28%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/var_fmt.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat 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- | ^~ -/usr/bin/ar qc ../../ilib/libgeneral-writer.a "CMakeFiles/general-writer.dir/general-writer.cpp.o" "CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o" -/usr/bin/ranlib ../../ilib/libgeneral-writer.a -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 28%] Built target general-writer -make -f tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/build.make tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/DependInfo.cmake --color= -cd 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-I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o -MF CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o.d -o CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/check-corrupt.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv abi-dump abi-dump.3.0.3 -[ 29%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-tools.c -[ 29%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump.c.o -MF CMakeFiles/sam-dump.dir/sam-dump.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-dump.3.0.3 abi-dump.3 /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c: In function 'KTUI_Menu_Remove_Id': /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c:408:22: warning: 'idx' may be used uninitialized [-Wmaybe-uninitialized] 408 | rc = VectorRemove ( &parent->children, idx, &removed ); @@ -3726,81 +3639,58 @@ /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c:401:22: note: 'idx' was declared here 401 | uint32_t idx; | ^~~ -[ 29%] Built target sff-dump -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-dump.3 abi-dump -make -f tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 29%] Built target abi-dump -make -f tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/DependInfo.cmake --color= -[ 29%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o -cd 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illumina-dump illumina-dump.3.0.3 -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-dump.3.0.3 illumina-dump.3 -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-dump.3 illumina-dump +[ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump-opts.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump-opts.c.o -MF CMakeFiles/sam-dump.dir/sam-dump-opts.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump-opts.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump-opts.c +[ 26%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/abi.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/abi.c.o -MF CMakeFiles/abi-dump.dir/abi.c.o.d -o CMakeFiles/abi-dump.dir/abi.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/abi.c +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 1010 | ReportBuildDate ( __DATE__ ); + | ^~~~~~~~ +[ 26%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_palette.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_palette.c.o -MF CMakeFiles/tui.dir/tui_palette.c.o.d -o CMakeFiles/tui.dir/tui_palette.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_palette.c +[ 26%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o -MF CMakeFiles/fasterq-dump.dir/tool_ctx.c.o.d -o CMakeFiles/fasterq-dump.dir/tool_ctx.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/tool_ctx.c +[ 26%] Linking C executable ../../../bin/sff-dump +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/sff-dump.dir/link.txt --verbose=1 +[ 26%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_std_dlg.c.o +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sff-dump.dir/factory.c.o" "CMakeFiles/sff-dump.dir/fasta_dump.c.o" "CMakeFiles/sff-dump.dir/core.c.o" "CMakeFiles/sff-dump.dir/sff.c.o" -o ../../../bin/sff-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_std_dlg.c.o -MF CMakeFiles/tui.dir/tui_std_dlg.c.o.d -o CMakeFiles/tui.dir/tui_std_dlg.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_std_dlg.c +[ 26%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-tools.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sff-dump.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sff-dump sff-dump.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-dump.3.0.3 sff-dump.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-dump.3 sff-dump make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 29%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o -MF CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o.d -o CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/vdb-encrypt.c -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'DumpQuality': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:1096:37: warning: the comparison will always evaluate as 'true' for the address of 'qualQuant' will never be NULL [-Waddress] - 1096 | char const newValue = ((param->qualQuant && param->qualQuantSingle)?param->qualQuantSingle:30) + 33; - | ^~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:205:13: note: 'qualQuant' declared here - 205 | uint8_t qualQuant[256]; - | ^~~~~~~~~ -[ 29%] Built target illumina-dump -make -f tools/external/srapath/CMakeFiles/srapath.dir/build.make tools/external/srapath/CMakeFiles/srapath.dir/depend +[ 26%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fastq.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD 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tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget.c.o -MF CMakeFiles/tui.dir/tui_widget.c.o.d -o CMakeFiles/tui.dir/tui_widget.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget.c +[ 26%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceIteratorItf.cpp +[ 26%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-str.c +[ 26%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/illumina.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/illumina.c.o -MF CMakeFiles/illumina-dump.dir/illumina.c.o.d -o CMakeFiles/illumina-dump.dir/illumina.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/illumina.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceIteratorItf.cpp:30: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +make -f tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/build.make tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/srapath /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath/CMakeFiles/srapath.dir/DependInfo.cmake --color= +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/DependInfo.cmake --color= +[ 26%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/inspector.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/inspector.c.o -MF CMakeFiles/fasterq-dump.dir/inspector.c.o.d -o CMakeFiles/fasterq-dump.dir/inspector.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/inspector.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/srapath/CMakeFiles/srapath.dir/build.make tools/external/srapath/CMakeFiles/srapath.dir/build +make -f tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/build.make tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'SetupColumns': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:3230:10: warning: the comparison will always evaluate as 'true' for the address of 'qualQuant' will never be NULL [-Waddress] - 3230 | if ( param -> qualQuant && param -> qualQuantSingle ) { /** we don't really need quality ***/ - | ^~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:205:13: note: 'qualQuant' declared here - 205 | uint8_t qualQuant[256]; - | ^~~~~~~~~ -[ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_palette.c.o -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'cg_canonical_print_cigar': -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_palette.c.o -MF CMakeFiles/tui.dir/tui_palette.c.o.d -o CMakeFiles/tui.dir/tui_palette.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_palette.c -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'SAM_Dump_Main': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1579:12: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] - 1579 | return rc; - | ^~ -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1547:10: note: 'rc' was declared here - 1547 | rc_t rc; - | ^~ -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:4380:22: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 4380 | ReportBuildDate( __DATE__ ); - | ^~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1574:13: warning: 'total_cnt' may be used uninitialized [-Wmaybe-uninitialized] - 1574 | KOutMsg( "%d%c", total_cnt, op ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1549:16: note: 'total_cnt' was declared here - 1549 | int i, total_cnt, cnt; - | ^~~~~~~~~ -[ 30%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/helper.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb 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-I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/shared.c.o -MF CMakeFiles/vdb-decrypt.dir/shared.c.o.d -o CMakeFiles/vdb-decrypt.dir/shared.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/shared.c -[ 31%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/report_deletes.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/report_deletes.c.o -MF CMakeFiles/sra-pileup.dir/report_deletes.c.o.d -o CMakeFiles/sra-pileup.dir/report_deletes.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/report_deletes.c -[ 31%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/shared.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/shared.c.o -MF CMakeFiles/vdb-encrypt.dir/shared.c.o.d -o CMakeFiles/vdb-encrypt.dir/shared.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/shared.c -[ 31%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_std_dlg.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_std_dlg.c.o -MF CMakeFiles/tui.dir/tui_std_dlg.c.o.d -o CMakeFiles/tui.dir/tui_std_dlg.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_std_dlg.c +[ 26%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/out_redir.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/out_redir.c.o -MF CMakeFiles/sam-dump.dir/out_redir.c.o.d -o CMakeFiles/sam-dump.dir/out_redir.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/out_redir.c +[ 27%] Building CXX object tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-validate\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o -MF CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o.d -o CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/check-corrupt.cpp /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c: In function 'ric_align_generic.constprop': /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c:1393:12: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] 1393 | if (chunk == last) @@ -3808,14 +3698,6 @@ /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c:1384:17: note: 'last' was declared here 1384 | int64_t last; | ^~~~ -[ 31%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/flex_printer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/flex_printer.c.o -MF CMakeFiles/fasterq-dump.dir/flex_printer.c.o.d -o CMakeFiles/fasterq-dump.dir/flex_printer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/flex_printer.c -[ 31%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_regions.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_regions.c.o -MF CMakeFiles/sra-pileup.dir/ref_regions.c.o.d -o CMakeFiles/sra-pileup.dir/ref_regions.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_regions.c -[ 31%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget.c.o -MF CMakeFiles/tui.dir/tui_widget.c.o.d -o CMakeFiles/tui.dir/tui_widget.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget.c -[ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_button.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_button.c.o -MF CMakeFiles/tui.dir/tui_widget_button.c.o.d -o CMakeFiles/tui.dir/tui_widget_button.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_button.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'cg_canonical_print_cigar': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1579:12: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 1579 | return rc; @@ -3829,96 +3711,254 @@ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1549:16: note: 'total_cnt' was declared here 1549 | int i, total_cnt, cnt; | ^~~~~~~~~ -[ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_dir.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_dir.c.o -MF CMakeFiles/fasterq-dump.dir/temp_dir.c.o.d -o CMakeFiles/fasterq-dump.dir/temp_dir.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/temp_dir.c -[ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_checkbox.c.o +[ 27%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr.c.o -MF CMakeFiles/sam-dump.dir/sam-hdr.c.o.d -o CMakeFiles/sam-dump.dir/sam-hdr.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-hdr.c +[ 28%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/report_deletes.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/report_deletes.c.o -MF CMakeFiles/sra-pileup.dir/report_deletes.c.o.d -o CMakeFiles/sra-pileup.dir/report_deletes.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/report_deletes.c +[ 28%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-helper.c +[ 28%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceSequenceItf.cpp +[ 28%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_regions.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_regions.c.o -MF CMakeFiles/sra-pileup.dir/ref_regions.c.o.d -o CMakeFiles/sra-pileup.dir/ref_regions.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_regions.c +[ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_button.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_button.c.o -MF CMakeFiles/tui.dir/tui_widget_button.c.o.d -o CMakeFiles/tui.dir/tui_widget_button.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_button.c +[ 29%] Linking C executable ../../../bin/illumina-dump +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/illumina-dump.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/illumina-dump.dir/factory.c.o" "CMakeFiles/illumina-dump.dir/fasta_dump.c.o" "CMakeFiles/illumina-dump.dir/core.c.o" "CMakeFiles/illumina-dump.dir/illumina.c.o" -o ../../../bin/illumina-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceSequenceItf.cpp:30: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f illumina-dump.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv illumina-dump illumina-dump.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-dump.3.0.3 illumina-dump.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-dump.3 illumina-dump +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 29%] Built target illumina-dump +make -f tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/DependInfo.cmake --color= +[ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_checkbox.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_checkbox.c.o -MF CMakeFiles/tui.dir/tui_widget_checkbox.c.o.d -o CMakeFiles/tui.dir/tui_widget_checkbox.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_checkbox.c -[ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump3.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump3.c.o -MF CMakeFiles/sam-dump.dir/sam-dump3.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump3.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c -[ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/dyn_string.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/dyn_string.c.o -MF CMakeFiles/sam-dump.dir/dyn_string.c.o.d -o CMakeFiles/sam-dump.dir/dyn_string.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/dyn_string.c -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c: In function 'KMain': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:557:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 557 | ReportBuildDate( __DATE__ ); - | ^~~~~~~~ -[ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/progress_thread.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/progress_thread.c.o -MF CMakeFiles/fasterq-dump.dir/progress_thread.c.o.d -o CMakeFiles/fasterq-dump.dir/progress_thread.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/progress_thread.c -[ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_grid.c.o +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 29%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr1.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr1.c.o -MF CMakeFiles/sam-dump.dir/sam-hdr1.c.o.d -o CMakeFiles/sam-dump.dir/sam-hdr1.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-hdr1.c +[ 29%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o -MF CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o.d -o CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/vdb-decrypt.c +[ 29%] Linking C executable ../../../bin/abi-dump +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/abi-dump.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/abi-dump.dir/factory.c.o" "CMakeFiles/abi-dump.dir/fasta_dump.c.o" "CMakeFiles/abi-dump.dir/core.c.o" "CMakeFiles/abi-dump.dir/abi.c.o" -o ../../../bin/abi-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_grid.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_grid.c.o -MF CMakeFiles/tui.dir/tui_widget_grid.c.o.d -o CMakeFiles/tui.dir/tui_widget_grid.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_grid.c -[ 32%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/line_iter.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/line_iter.c.o -MF CMakeFiles/srapath.dir/line_iter.c.o.d -o CMakeFiles/srapath.dir/line_iter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/line_iter.c -In function 'samdump_main', - inlined from 'KMain' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:558:26: -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:510:10: warning: 'mode' may be used uninitialized [-Wmaybe-uninitialized] - 510 | rc = init_out_redir( &redir, mode, opts->outputfile, opts->output_buffer_size ); /* from out_redir.c */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c: In function 'KMain': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:502:25: note: 'mode' was declared here - 502 | enum out_redir_mode mode; - | ^~~~ -[ 32%] Linking C executable ../../../bin/vdb-decrypt +[ 29%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/matecache.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/matecache.c.o -MF CMakeFiles/sam-dump.dir/matecache.c.o.d -o CMakeFiles/sam-dump.dir/matecache.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/matecache.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f abi-dump.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv abi-dump abi-dump.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-dump.3.0.3 abi-dump.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-dump.3 abi-dump +[ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_inputline.c.o +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_inputline.c.o -MF CMakeFiles/tui.dir/tui_widget_inputline.c.o.d -o CMakeFiles/tui.dir/tui_widget_inputline.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_inputline.c +[ 29%] Built target abi-dump +make -f tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 29%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/shared.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/shared.c.o -MF CMakeFiles/vdb-decrypt.dir/shared.c.o.d -o CMakeFiles/vdb-decrypt.dir/shared.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/shared.c +[ 29%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o -MF CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o.d -o CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/vdb-encrypt.c +[ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_label.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_label.c.o -MF CMakeFiles/tui.dir/tui_widget_label.c.o.d -o CMakeFiles/tui.dir/tui_widget_label.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_label.c +[ 29%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/shared.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/shared.c.o -MF CMakeFiles/vdb-encrypt.dir/shared.c.o.d -o CMakeFiles/vdb-encrypt.dir/shared.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/shared.c +[ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_progress.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_progress.c.o -MF CMakeFiles/tui.dir/tui_widget_progress.c.o.d -o CMakeFiles/tui.dir/tui_widget_progress.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_progress.c +[ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sbuffer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sbuffer.c.o -MF CMakeFiles/fasterq-dump.dir/sbuffer.c.o.d -o CMakeFiles/fasterq-dump.dir/sbuffer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/sbuffer.c +[ 29%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-formats.c +[ 29%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/read_fkt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/read_fkt.c.o -MF CMakeFiles/sam-dump.dir/read_fkt.c.o.d -o CMakeFiles/sam-dump.dir/read_fkt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/read_fkt.c +[ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_radiobox.c.o +[ 29%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/4na_ascii.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_radiobox.c.o -MF CMakeFiles/tui.dir/tui_widget_radiobox.c.o.d -o CMakeFiles/tui.dir/tui_widget_radiobox.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_radiobox.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/4na_ascii.c.o -MF CMakeFiles/sra-pileup.dir/4na_ascii.c.o.d -o CMakeFiles/sra-pileup.dir/4na_ascii.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/4na_ascii.c +[ 29%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StatisticsItf.cpp +[ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_spin_edit.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_spin_edit.c.o -MF CMakeFiles/tui.dir/tui_widget_spin_edit.c.o.d -o CMakeFiles/tui.dir/tui_widget_spin_edit.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_spin_edit.c +[ 29%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o -MF CMakeFiles/sra-pileup.dir/ref_walker_0.c.o.d -o CMakeFiles/sra-pileup.dir/ref_walker_0.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker_0.c +[ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/err_msg.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/err_msg.c.o -MF CMakeFiles/fasterq-dump.dir/err_msg.c.o.d -o CMakeFiles/fasterq-dump.dir/err_msg.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/err_msg.c +[ 29%] Linking C executable ../../../bin/vdb-decrypt cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-decrypt.dir/link.txt --verbose=1 +[ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_string_list.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_string_list.c.o -MF CMakeFiles/tui.dir/tui_widget_string_list.c.o.d -o CMakeFiles/tui.dir/tui_widget_string_list.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_string_list.c +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StatisticsItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StatisticsItf.cpp:30: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o" "CMakeFiles/vdb-decrypt.dir/shared.c.o" -o ../../../bin/vdb-decrypt /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_tools.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_tools.c.o -MF CMakeFiles/fasterq-dump.dir/file_tools.c.o.d -o CMakeFiles/fasterq-dump.dir/file_tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/file_tools.c +[ 30%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_tabhdr.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_tabhdr.c.o -MF CMakeFiles/tui.dir/tui_widget_tabhdr.c.o.d -o CMakeFiles/tui.dir/tui_widget_tabhdr.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_tabhdr.c +[ 30%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-aligned.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-aligned.c.o -MF CMakeFiles/sam-dump.dir/sam-aligned.c.o.d -o CMakeFiles/sam-dump.dir/sam-aligned.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-aligned.c +[ 30%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-redir.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-decrypt.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-decrypt vdb-decrypt.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-decrypt.3.0.3 vdb-decrypt.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-decrypt.3 vdb-decrypt +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 30%] Built target vdb-decrypt +make -f tools/external/srapath/CMakeFiles/srapath.dir/build.make tools/external/srapath/CMakeFiles/srapath.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/srapath /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath/CMakeFiles/srapath.dir/DependInfo.cmake --color= +[ 30%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/linux/systui.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/linux/systui.c.o -MF CMakeFiles/tui.dir/linux/systui.c.o.d -o CMakeFiles/tui.dir/linux/systui.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/linux/systui.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/external/srapath/CMakeFiles/srapath.dir/build.make tools/external/srapath/CMakeFiles/srapath.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 31%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o +[ 31%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/helper.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/helper.c.o -MF CMakeFiles/srapath.dir/helper.c.o.d -o CMakeFiles/srapath.dir/helper.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/helper.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o -MF CMakeFiles/sra-pileup.dir/ref_walker.c.o.d -o CMakeFiles/sra-pileup.dir/ref_walker.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c +[ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/var_fmt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/var_fmt.c.o -MF CMakeFiles/fasterq-dump.dir/var_fmt.c.o.d -o CMakeFiles/fasterq-dump.dir/var_fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/var_fmt.c [ 32%] Linking C executable ../../../bin/vdb-encrypt cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-encrypt.dir/link.txt --verbose=1 -[ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/4na_ascii.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/4na_ascii.c.o -MF CMakeFiles/sra-pileup.dir/4na_ascii.c.o.d -o CMakeFiles/sra-pileup.dir/4na_ascii.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/4na_ascii.c -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o" "CMakeFiles/vdb-decrypt.dir/shared.c.o" -o ../../../bin/vdb-decrypt /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o" "CMakeFiles/vdb-encrypt.dir/shared.c.o" -o ../../../bin/vdb-encrypt /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o +[ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/flex_printer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/flex_printer.c.o -MF CMakeFiles/fasterq-dump.dir/flex_printer.c.o.d -o CMakeFiles/fasterq-dump.dir/flex_printer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/flex_printer.c +[ 32%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-fastq.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-encrypt.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-encrypt vdb-encrypt.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-encrypt.3.0.3 vdb-encrypt.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-encrypt.3 vdb-encrypt +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 32%] Built target vdb-encrypt make -f tools/external/sra-stat/CMakeFiles/sra-stat.dir/build.make tools/external/sra-stat/CMakeFiles/sra-stat.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-stat /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat/CMakeFiles/sra-stat.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o -MF CMakeFiles/sra-pileup.dir/ref_walker_0.c.o.d -o CMakeFiles/sra-pileup.dir/ref_walker_0.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker_0.c -[ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o -MF CMakeFiles/sra-pileup.dir/ref_walker.c.o.d -o CMakeFiles/sra-pileup.dir/ref_walker.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c +In function 'make_cursor_ids', + inlined from 'ref_walker_add_iterator.constprop' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:591:15: +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:534:14: warning: 'ids' may be used uninitialized [-Wmaybe-uninitialized] + 534 | rc = VectorAppend ( cursor_id_vector, NULL, ids ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:34: +/usr/include/ncbi-vdb/klib/vector.h: In function 'ref_walker_add_iterator.constprop': +/usr/include/ncbi-vdb/klib/vector.h:401:21: note: by argument 3 of type 'const void *' to 'VectorAppend' declared here + 401 | KLIB_EXTERN rc_t CC VectorAppend ( Vector *self, uint32_t *idx, const void *item ); + | ^~~~~~~~~~~~ +[ 33%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-unaligned.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-unaligned.c.o -MF CMakeFiles/sam-dump.dir/sam-unaligned.c.o.d -o CMakeFiles/sam-dump.dir/sam-unaligned.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-stat/CMakeFiles/sra-stat.dir/build.make tools/external/sra-stat/CMakeFiles/sra-stat.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 32%] Building C object tools/external/sra-stat/CMakeFiles/sra-stat.dir/assembly-statistics.c.o +[ 33%] Building C object tools/external/sra-stat/CMakeFiles/sra-stat.dir/assembly-statistics.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-stat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-stat/CMakeFiles/sra-stat.dir/assembly-statistics.c.o -MF CMakeFiles/sra-stat.dir/assembly-statistics.c.o.d -o CMakeFiles/sra-stat.dir/assembly-statistics.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-stat/assembly-statistics.c -[ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cleanup_task.c.o +[ 33%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_dir.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_dir.c.o -MF CMakeFiles/fasterq-dump.dir/temp_dir.c.o.d -o CMakeFiles/fasterq-dump.dir/temp_dir.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/temp_dir.c +[ 33%] Linking C executable ../../../bin/fastq-dump +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastq-dump.dir/link.txt --verbose=1 +[ 33%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/fastq-dump.dir/factory.c.o" "CMakeFiles/fastq-dump.dir/fasta_dump.c.o" "CMakeFiles/fastq-dump.dir/core.c.o" "CMakeFiles/fastq-dump.dir/fastq.c.o" -o ../../../bin/fastq-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_Refcount.cpp +[ 33%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/progress_thread.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/progress_thread.c.o -MF CMakeFiles/fasterq-dump.dir/progress_thread.c.o.d -o CMakeFiles/fasterq-dump.dir/progress_thread.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/progress_thread.c +[ 34%] Linking C executable ../../../bin/vdb-validate +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-validate.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-validate.dir/vdb-validate.c.o" -o ../../../bin/vdb-validate /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 34%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cleanup_task.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastq-dump.3.0.3 +[ 34%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/line_iter.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cleanup_task.c.o -MF CMakeFiles/fasterq-dump.dir/cleanup_task.c.o.d -o CMakeFiles/fasterq-dump.dir/cleanup_task.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/cleanup_task.c -[ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/walk_debug.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/walk_debug.c.o -MF CMakeFiles/sra-pileup.dir/walk_debug.c.o.d -o CMakeFiles/sra-pileup.dir/walk_debug.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/walk_debug.c -[ 32%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/repository-mgr.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/repository-mgr.c.o -MF CMakeFiles/srapath.dir/repository-mgr.c.o.d -o CMakeFiles/srapath.dir/repository-mgr.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/repository-mgr.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-decrypt.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-decrypt vdb-decrypt.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-decrypt.3.0.3 vdb-decrypt.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-encrypt.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-decrypt.3 vdb-decrypt -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-encrypt vdb-encrypt.3.0.3 -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-encrypt.3.0.3 vdb-encrypt.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-encrypt.3 vdb-encrypt -[ 32%] Built target vdb-decrypt +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/line_iter.c.o -MF CMakeFiles/srapath.dir/line_iter.c.o.d -o CMakeFiles/srapath.dir/line_iter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/line_iter.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fastq-dump fastq-dump.3.0.3 +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_Refcount.cpp:30: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c: In function 'print_sliced_quality': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c:407:12: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] + 407 | return rc; + | ^~ +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c:391:10: note: 'rc' was declared here + 391 | rc_t rc; + | ^~ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-dump.3.0.3 fastq-dump.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-dump.3 fastq-dump +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 fastq-dump-driver +[ 34%] Linking C static library ../../../../ilib/libtui.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -P CMakeFiles/tui.dir/cmake_clean_target.cmake +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -E cmake_link_script CMakeFiles/tui.dir/link.txt --verbose=1 +[ 34%] Built target fastq-dump make -f tools/external/rcexplain/CMakeFiles/rcexplain.dir/build.make tools/external/rcexplain/CMakeFiles/rcexplain.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/rcexplain /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/rcexplain 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CMakeFiles/tui.dir/tui_widget_spin_edit.c.o CMakeFiles/tui.dir/tui_widget_string_list.c.o CMakeFiles/tui.dir/tui_widget_tabhdr.c.o CMakeFiles/tui.dir/linux/systui.c.o +[ 34%] Building C object tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-stat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra.c.o -MF CMakeFiles/sra-stat.dir/sra.c.o.d -o CMakeFiles/sra-stat.dir/sra.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-stat/sra.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/external/rcexplain/CMakeFiles/rcexplain.dir/build.make tools/external/rcexplain/CMakeFiles/rcexplain.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/usr/bin/ranlib ../../../../ilib/libtui.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-validate.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-validate vdb-validate.3.0.3 +[ 34%] Building C object tools/external/rcexplain/CMakeFiles/rcexplain.dir/rcexplain.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/rcexplain && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/util\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/rcexplain/CMakeFiles/rcexplain.dir/rcexplain.c.o -MF CMakeFiles/rcexplain.dir/rcexplain.c.o.d -o CMakeFiles/rcexplain.dir/rcexplain.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/rcexplain/rcexplain.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-validate.3.0.3 vdb-validate.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-validate.3 vdb-validate +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 34%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/walk_debug.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/walk_debug.c.o -MF CMakeFiles/sra-pileup.dir/walk_debug.c.o.d -o CMakeFiles/sra-pileup.dir/walk_debug.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/walk_debug.c +[ 34%] Built target vdb-validate +[ 34%] Built target tui make -f tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/build.make tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/kdbmeta /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/rcexplain/CMakeFiles/rcexplain.dir/build.make tools/external/rcexplain/CMakeFiles/rcexplain.dir/build +make -f tools/external/align-info/CMakeFiles/align-info.dir/build.make tools/external/align-info/CMakeFiles/align-info.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 32%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/services.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/services.c.o -MF CMakeFiles/srapath.dir/services.c.o.d -o CMakeFiles/srapath.dir/services.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/align-info /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/align-info /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/align-info/CMakeFiles/align-info.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/build.make tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/build -[ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/index.c.o +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/external/align-info/CMakeFiles/align-info.dir/build.make tools/external/align-info/CMakeFiles/align-info.dir/build +[ 34%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/index.c.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/index.c.o -MF CMakeFiles/fasterq-dump.dir/index.c.o.d -o CMakeFiles/fasterq-dump.dir/index.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/index.c -[ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_counters.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_counters.c.o -MF CMakeFiles/sra-pileup.dir/pileup_counters.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_counters.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_counters.c -[ 32%] Building C object tools/external/rcexplain/CMakeFiles/rcexplain.dir/rcexplain.c.o -cd 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/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/repository-mgr.c.o -MF CMakeFiles/srapath.dir/repository-mgr.c.o.d -o CMakeFiles/srapath.dir/repository-mgr.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/repository-mgr.c +[ 34%] Building C object tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/kdbmeta.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/util\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/kdbmeta.c.o -MF CMakeFiles/kdbmeta.dir/kdbmeta.c.o.d -o CMakeFiles/kdbmeta.dir/kdbmeta.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/kdbmeta/kdbmeta.c -[ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_label.c.o +[ 34%] Building C object tools/external/align-info/CMakeFiles/align-info.dir/align-info.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/align-info && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/align-info\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/align-info/CMakeFiles/align-info.dir/align-info.c.o -MF CMakeFiles/align-info.dir/align-info.c.o.d -o CMakeFiles/align-info.dir/align-info.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/align-info/align-info.c +[ 34%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_writer.c.o -MF CMakeFiles/fasterq-dump.dir/lookup_writer.c.o.d -o CMakeFiles/fasterq-dump.dir/lookup_writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/lookup_writer.c +[ 34%] Linking C executable ../../../bin/rcexplain +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/rcexplain && /usr/bin/cmake -E cmake_link_script CMakeFiles/rcexplain.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/rcexplain.dir/rcexplain.c.o -o ../../../bin/rcexplain /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 34%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/services.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/services.c.o -MF CMakeFiles/srapath.dir/services.c.o.d -o CMakeFiles/srapath.dir/services.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c +[ 34%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_counters.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_counters.c.o -MF CMakeFiles/sra-pileup.dir/pileup_counters.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_counters.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_counters.c +[ 34%] Linking CXX executable ../../../bin/check-corrupt +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cmake -E cmake_link_script CMakeFiles/check-corrupt.dir/link.txt --verbose=1 /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c: In function 'json_print_named_url': /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c:338:10: warning: unused variable 'rc' [-Wunused-variable] 338 | rc_t rc = VPathMakeString(url, &tmp); assert(rc == 0); @@ -3927,180 +3967,115 @@ /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c:356:14: warning: unused variable 'rc' [-Wunused-variable] 356 | rc_t rc = VPathMakeString(url, &tmp); assert(rc == 0); | ^~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_label.c.o -MF CMakeFiles/tui.dir/tui_widget_label.c.o.d -o CMakeFiles/tui.dir/tui_widget_label.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_label.c -In function 'make_cursor_ids', - inlined from 'ref_walker_add_iterator.constprop' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:591:15: -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:534:14: warning: 'ids' may be used uninitialized [-Wmaybe-uninitialized] - 534 | rc = VectorAppend ( cursor_id_vector, NULL, ids ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:34: -/usr/include/ncbi-vdb/klib/vector.h: In function 'ref_walker_add_iterator.constprop': -/usr/include/ncbi-vdb/klib/vector.h:401:21: note: by argument 3 of type 'const void *' to 'VectorAppend' declared here - 401 | KLIB_EXTERN rc_t CC VectorAppend ( Vector *self, uint32_t *idx, const void *item ); - | ^~~~~~~~~~~~ -[ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_index.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_index.c.o -MF CMakeFiles/sra-pileup.dir/pileup_index.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_index.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_index.c -[ 32%] Building C object tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-stat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux 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-I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_progress.c.o -MF CMakeFiles/tui.dir/tui_widget_progress.c.o.d -o CMakeFiles/tui.dir/tui_widget_progress.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_progress.c -[ 32%] Linking C executable ../../../bin/rcexplain -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/rcexplain && /usr/bin/cmake -E cmake_link_script CMakeFiles/rcexplain.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/rcexplain.dir/rcexplain.c.o -o 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-c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_varcount.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f rcexplain.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv rcexplain rcexplain.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rcexplain.3.0.3 rcexplain.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rcexplain.3 rcexplain make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 33%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_spin_edit.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk 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tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_string_list.c.o -MF CMakeFiles/tui.dir/tui_widget_string_list.c.o.d -o CMakeFiles/tui.dir/tui_widget_string_list.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_string_list.c -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/align-info/CMakeFiles/align-info.dir/build.make tools/external/align-info/CMakeFiles/align-info.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 33%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_v2.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix 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-I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/linux/systui.c.o -MF CMakeFiles/tui.dir/linux/systui.c.o.d -o CMakeFiles/tui.dir/linux/systui.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/linux/systui.c -[ 34%] Linking CXX executable ../../../bin/check-corrupt -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cmake -E cmake_link_script CMakeFiles/check-corrupt.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o" -o ../../../bin/check-corrupt /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 34%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/cgi_request.c.o +[ 34%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_reader.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall 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CMakeFiles/fastq-dump.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/srapath.c.o -MF CMakeFiles/srapath.dir/srapath.c.o.d -o CMakeFiles/srapath.dir/srapath.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/srapath.c -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time 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tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra-stat.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-stat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra-stat.c.o -MF CMakeFiles/sra-stat.dir/sra-stat.c.o.d -o CMakeFiles/sra-stat.dir/sra-stat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-stat/sra-stat.c +[ 34%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o +cd 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tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_file_list.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_file_list.c.o -MF CMakeFiles/fasterq-dump.dir/locked_file_list.c.o.d -o CMakeFiles/fasterq-dump.dir/locked_file_list.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/locked_file_list.c -/usr/bin/cc -g -O2 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CMakeFiles/kdbmeta.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastq-dump.3.0.3 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/kdbmeta.dir/kdbmeta.c.o -o ../../../bin/kdbmeta /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -[ 36%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_value.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fastq-dump fastq-dump.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_value.c.o -MF CMakeFiles/fasterq-dump.dir/locked_value.c.o.d -o CMakeFiles/fasterq-dump.dir/locked_value.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/locked_value.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-dump.3.0.3 fastq-dump.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-dump.3 fastq-dump -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 fastq-dump-driver cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f check-corrupt.3.0.3 -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv check-corrupt check-corrupt.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s check-corrupt.3.0.3 check-corrupt.3 -[ 36%] Built target fastq-dump -make -f tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/build.make tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/depend cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s check-corrupt.3 check-corrupt +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 35%] Built target check-corrupt +make -f tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/build.make tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr 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-I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_printer.c.o -MF CMakeFiles/fasterq-dump.dir/file_printer.c.o.d -o CMakeFiles/fasterq-dump.dir/file_printer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/file_printer.c +[ 37%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_indels.c.o +[ 37%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb_info.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_indels.c.o -MF CMakeFiles/sra-pileup.dir/pileup_indels.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_indels.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_indels.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb_info.c.o -MF CMakeFiles/vdb-dump.dir/vdb_info.c.o.d -o CMakeFiles/vdb-dump.dir/vdb_info.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c +[ 38%] Linking C executable ../../../bin/align-info +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/align-info && /usr/bin/cmake -E cmake_link_script CMakeFiles/align-info.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/align-info.dir/align-info.c.o" -o ../../../bin/align-info /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/merge_sorter.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/merge_sorter.c.o -MF CMakeFiles/fasterq-dump.dir/merge_sorter.c.o.d -o CMakeFiles/fasterq-dump.dir/merge_sorter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/merge_sorter.c +[ 38%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_varcount.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_varcount.c.o -MF CMakeFiles/sra-pileup.dir/pileup_varcount.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_varcount.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_varcount.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f align-info.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv align-info align-info.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-info.3.0.3 align-info.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-info.3 align-info make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/driver-tool/CMakeFiles/sratools.dir/build.make tools/external/driver-tool/CMakeFiles/sratools.dir/build +[ 38%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_stat.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_stat.c.o -MF CMakeFiles/sra-pileup.dir/pileup_stat.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_stat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_stat.c +[ 38%] Built target align-info +make -f tools/external/driver-tool/CMakeFiles/sratools.dir/build.make tools/external/driver-tool/CMakeFiles/sratools.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kdbmeta.3.0.3 -[ 37%] Building C object tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/cache-mgr.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cache-mgr\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/cache-mgr.c.o -MF CMakeFiles/cache-mgr.dir/cache-mgr.c.o.d -o CMakeFiles/cache-mgr.dir/cache-mgr.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kdbmeta kdbmeta.3.0.3 -[ 37%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/sratools.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdbmeta.3.0.3 kdbmeta.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/sratools.cpp.o -MF CMakeFiles/sratools.dir/sratools.cpp.o.d -o CMakeFiles/sratools.dir/sratools.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp -[ 37%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/merge_sorter.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdbmeta.3 kdbmeta +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool/CMakeFiles/sratools.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/merge_sorter.c.o -MF CMakeFiles/fasterq-dump.dir/merge_sorter.c.o.d -o CMakeFiles/fasterq-dump.dir/merge_sorter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/merge_sorter.c -[ 37%] Built target kdbmeta -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-validate.3.0.3 +make -f tools/external/driver-tool/CMakeFiles/sratools.dir/build.make tools/external/driver-tool/CMakeFiles/sratools.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/bam-loader/CMakeFiles/bam-load.dir/build.make tools/loaders/bam-loader/CMakeFiles/bam-load.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader/CMakeFiles/bam-load.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-validate vdb-validate.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-validate.3.0.3 vdb-validate.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-validate.3 vdb-validate -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 38%] Linking C executable ../../../bin/align-info +[ 38%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/sratools.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/sratools.cpp.o -MF CMakeFiles/sratools.dir/sratools.cpp.o.d -o CMakeFiles/sratools.dir/sratools.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/align-info && /usr/bin/cmake -E cmake_link_script CMakeFiles/align-info.dir/link.txt --verbose=1 make -f tools/loaders/bam-loader/CMakeFiles/bam-load.dir/build.make tools/loaders/bam-loader/CMakeFiles/bam-load.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/bam-loader/CMakeFiles/samview.dir/build.make tools/loaders/bam-loader/CMakeFiles/samview.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader/CMakeFiles/samview.dir/DependInfo.cmake --color= -[ 38%] Built target vdb-validate -make -f tools/loaders/kar/CMakeFiles/kar.dir/build.make tools/loaders/kar/CMakeFiles/kar.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar.dir/DependInfo.cmake --color= -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/align-info.dir/align-info.c.o" -o ../../../bin/align-info /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 38%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/bam-loader.c.o -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/bam-loader/CMakeFiles/samview.dir/build.make tools/loaders/bam-loader/CMakeFiles/samview.dir/build cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/bam-loader.c.o -MF CMakeFiles/bam-load.dir/bam-loader.c.o.d -o CMakeFiles/bam-load.dir/bam-loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/kar/CMakeFiles/kar.dir/build.make tools/loaders/kar/CMakeFiles/kar.dir/build -[ 38%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/bam.c.o -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/bam.c.o -MF CMakeFiles/samview.dir/bam.c.o.d -o CMakeFiles/samview.dir/bam.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c -[ 38%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar-path.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar.dir/kar-path.c.o -MF CMakeFiles/kar.dir/kar-path.c.o.d -o CMakeFiles/kar.dir/kar-path.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar-path.c -[ 38%] Linking C executable ../../../bin/sra-pileup -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-pileup.dir/link.txt --verbose=1 -[ 38%] Linking C static library ../../../../ilib/libtui.a +[ 38%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/md_flag.c.o +[ 38%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_v2.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/md_flag.c.o -MF CMakeFiles/sam-dump.dir/md_flag.c.o.d -o CMakeFiles/sam-dump.dir/md_flag.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/md_flag.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_v2.c.o -MF CMakeFiles/sra-pileup.dir/pileup_v2.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_v2.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_v2.c +In function 'inspect_line', + inlined from 'parse_buffer' at /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:602:29, + inlined from 'get_meta_bam_hdr' at /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:639:21, + inlined from 'get_meta_info' at /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:681:5: +/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:575:43: warning: 'line' may be used uninitialized [-Wmaybe-uninitialized] + 575 | case 'P' : if ( 'G' == line[ 2 ] ) ( bam_hdr -> PG_lines )++; break; + | ~~~~^~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c: In function 'get_meta_info': +/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:582:12: note: 'line' was declared here + 582 | char * line; + | ^~~~ +[ 38%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/sra-pileup.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/sra-pileup.c.o -MF CMakeFiles/sra-pileup.dir/sra-pileup.c.o.d -o CMakeFiles/sra-pileup.dir/sra-pileup.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sra-pileup.c +[ 38%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/cgi_request.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/cgi_request.c.o -MF CMakeFiles/srapath.dir/cgi_request.c.o.d -o CMakeFiles/srapath.dir/cgi_request.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/cgi_request.c +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sra-pileup.c: In function 'KMain': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sra-pileup.c:1415:22: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 1415 | ReportBuildDate( __DATE__ ); + | ^~~~~~~~ +[ 38%] Linking C executable ../../../bin/kdbmeta +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta && /usr/bin/cmake -E cmake_link_script CMakeFiles/kdbmeta.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/kdbmeta.dir/kdbmeta.c.o -o ../../../bin/kdbmeta /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c: In function 'rc_t Usage(const Args*)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:579:18: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 579 | for(i = 0; i < argsQty; i++ ) { @@ -4108,8 +4083,8 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:585:18: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 585 | for(i = 0; i < argsQty; i++ ) { | ~~^~~~~~~~~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -P CMakeFiles/tui.dir/cmake_clean_target.cmake -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-pileup.dir/dyn_string.c.o" "CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o" "CMakeFiles/sra-pileup.dir/out_redir.c.o" "CMakeFiles/sra-pileup.dir/perf_log.c.o" "CMakeFiles/sra-pileup.dir/reref.c.o" "CMakeFiles/sra-pileup.dir/cg_tools.c.o" "CMakeFiles/sra-pileup.dir/report_deletes.c.o" "CMakeFiles/sra-pileup.dir/ref_regions.c.o" "CMakeFiles/sra-pileup.dir/4na_ascii.c.o" "CMakeFiles/sra-pileup.dir/ref_walker_0.c.o" "CMakeFiles/sra-pileup.dir/ref_walker.c.o" "CMakeFiles/sra-pileup.dir/walk_debug.c.o" "CMakeFiles/sra-pileup.dir/pileup_counters.c.o" "CMakeFiles/sra-pileup.dir/pileup_index.c.o" "CMakeFiles/sra-pileup.dir/pileup_indels.c.o" "CMakeFiles/sra-pileup.dir/pileup_varcount.c.o" "CMakeFiles/sra-pileup.dir/pileup_stat.c.o" "CMakeFiles/sra-pileup.dir/pileup_v2.c.o" "CMakeFiles/sra-pileup.dir/sra-pileup.c.o" -o ../../../bin/sra-pileup /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 38%] Linking C executable ../../../bin/cache-mgr +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr && /usr/bin/cmake -E cmake_link_script CMakeFiles/cache-mgr.dir/link.txt --verbose=1 /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c: In function 'rc_t KMain(int, char**)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:1304:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1304 | argv[1] = "--help"; @@ -4117,154 +4092,135 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:1309:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1309 | argv[1] = "--version"; | ^~~~~~~~~~~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -E cmake_link_script CMakeFiles/tui.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/cache-mgr.dir/cache-mgr.c.o" -o ../../../bin/cache-mgr /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 38%] Linking CXX static library ../../../../ilib/libngs-bind-python.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/cmake -P CMakeFiles/ngs-bind-python.dir/cmake_clean_target.cmake +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kdbmeta.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kdbmeta kdbmeta.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-python.dir/link.txt --verbose=1 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdbmeta.3.0.3 kdbmeta.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdbmeta.3 kdbmeta +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/usr/bin/ar qc ../../../../ilib/libngs-bind-python.a "CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o" +[ 38%] Built target kdbmeta +make -f tools/loaders/bam-loader/CMakeFiles/samview.dir/build.make tools/loaders/bam-loader/CMakeFiles/samview.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader/CMakeFiles/samview.dir/DependInfo.cmake --color= +/usr/bin/ranlib ../../../../ilib/libngs-bind-python.a +[ 38%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/cg_tools.c.o [ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sorter.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sorter.c.o -MF CMakeFiles/fasterq-dump.dir/sorter.c.o.d -o CMakeFiles/fasterq-dump.dir/sorter.c.o -c 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-/usr/bin/ranlib ../../../../ilib/libtui.a -[ 38%] Linking C executable ../../../bin/srapath -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f align-info.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cmake -E cmake_link_script CMakeFiles/srapath.dir/link.txt --verbose=1 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/cg_tools.c.o -MF CMakeFiles/sam-dump.dir/cg_tools.c.o.d -o CMakeFiles/sam-dump.dir/cg_tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f cache-mgr.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv align-info align-info.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-info.3.0.3 align-info.3 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/srapath.dir/helper.c.o CMakeFiles/srapath.dir/line_iter.c.o "CMakeFiles/srapath.dir/repository-mgr.c.o" CMakeFiles/srapath.dir/services.c.o CMakeFiles/srapath.dir/cgi_request.c.o CMakeFiles/srapath.dir/srapath.c.o -o ../../../bin/srapath /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 38%] Built target tui -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-info.3 align-info +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv cache-mgr cache-mgr.3.0.3 +make -f tools/loaders/bam-loader/CMakeFiles/samview.dir/build.make tools/loaders/bam-loader/CMakeFiles/samview.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cache-mgr.3.0.3 cache-mgr.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cache-mgr.3 cache-mgr +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 38%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/bam.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/bam.c.o -MF CMakeFiles/samview.dir/bam.c.o.d -o CMakeFiles/samview.dir/bam.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c +[ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cmn_iter.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cmn_iter.c.o -MF CMakeFiles/fasterq-dump.dir/cmn_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/cmn_iter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/cmn_iter.c +[ 38%] Built target ngs-bind-python +make -f tools/loaders/kar/CMakeFiles/kar.dir/build.make tools/loaders/kar/CMakeFiles/kar.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar.dir/DependInfo.cmake --color= +[ 38%] Built target cache-mgr make -f tools/loaders/kar/CMakeFiles/kar+.dir/build.make tools/loaders/kar/CMakeFiles/kar+.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar+.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 38%] Built target align-info -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-pileup.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-pileup sra-pileup.3.0.3 -make -f tools/loaders/kar/CMakeFiles/kar+meta.dir/build.make tools/loaders/kar/CMakeFiles/kar+meta.dir/depend +make -f tools/loaders/kar/CMakeFiles/kar.dir/build.make tools/loaders/kar/CMakeFiles/kar.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar+meta.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-pileup.3.0.3 sra-pileup.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/kar/CMakeFiles/kar+.dir/build.make tools/loaders/kar/CMakeFiles/kar+.dir/build +[ 38%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar-path.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar.dir/kar-path.c.o -MF CMakeFiles/kar.dir/kar-path.c.o.d -o CMakeFiles/kar.dir/kar-path.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar-path.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-pileup.3 sra-pileup -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sra-pileup-driver -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'fmt_cigar_elem': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:491:10: warning: unused variable 'rc' [-Wunused-variable] + 491 | rc_t rc = string_printf ( dst, 11, &num_writ, "%d%c", cig_oplen, cig_op ); + | ^~ [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar-path.c.o -make -f tools/loaders/kar/CMakeFiles/kar+meta.dir/build.make tools/loaders/kar/CMakeFiles/kar+meta.dir/build cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar-path.c.o -MF CMakeFiles/kar+.dir/kar-path.c.o.d -o CMakeFiles/kar+.dir/kar-path.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar-path.c -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 38%] Built target sra-pileup -make -f tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build.make tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/DependInfo.cmake --color= -[ 38%] Building C object tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+util.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+util.c.o -MF CMakeFiles/kar+meta.dir/kar+util.c.o.d -o CMakeFiles/kar+meta.dir/kar+util.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+util.c -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build.make tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 38%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar-args.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f srapath.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar.dir/kar-args.c.o -MF CMakeFiles/kar.dir/kar-args.c.o.d -o CMakeFiles/kar.dir/kar-args.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar-args.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv srapath srapath.3.0.3 -[ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cmn_iter.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srapath.3.0.3 srapath.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cmn_iter.c.o -MF CMakeFiles/fasterq-dump.dir/cmn_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/cmn_iter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/cmn_iter.c -[ 38%] Building C object tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o -MF CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o.d -o CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/dump-blob-boundaries.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srapath.3 srapath [ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o -MF CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/raw_read_iter.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 srapath-driver -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 38%] Built target srapath -make -f tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/DependInfo.cmake --color= -[ 38%] Linking C executable ../../../bin/cache-mgr -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr && /usr/bin/cmake -E cmake_link_script CMakeFiles/cache-mgr.dir/link.txt --verbose=1 -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/cache-mgr.dir/cache-mgr.c.o" -o ../../../bin/cache-mgr /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 38%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/caps.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/caps.c.o -MF CMakeFiles/sra-sort.dir/caps.c.o.d -o CMakeFiles/sra-sort.dir/caps.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/caps.c -[ 38%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar.dir/kar.c.o -MF CMakeFiles/kar.dir/kar.c.o.d -o CMakeFiles/kar.dir/kar.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c +[ 38%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump.c +[ 38%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar-args.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong 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cache-mgr.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam-dump.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cache-mgr.3.0.3 cache-mgr.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cache-mgr.3 cache-mgr -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sam-dump.dir/inputfiles.c.o" "CMakeFiles/sam-dump.dir/perf_log.c.o" "CMakeFiles/sam-dump.dir/rna_splice_log.c.o" "CMakeFiles/sam-dump.dir/sam-dump-opts.c.o" "CMakeFiles/sam-dump.dir/out_redir.c.o" "CMakeFiles/sam-dump.dir/sam-hdr.c.o" "CMakeFiles/sam-dump.dir/sam-hdr1.c.o" "CMakeFiles/sam-dump.dir/matecache.c.o" "CMakeFiles/sam-dump.dir/read_fkt.c.o" "CMakeFiles/sam-dump.dir/sam-aligned.c.o" "CMakeFiles/sam-dump.dir/sam-unaligned.c.o" "CMakeFiles/sam-dump.dir/md_flag.c.o" "CMakeFiles/sam-dump.dir/cg_tools.c.o" "CMakeFiles/sam-dump.dir/sam-dump.c.o" "CMakeFiles/sam-dump.dir/sam-dump3.c.o" "CMakeFiles/sam-dump.dir/dyn_string.c.o" -o ../../../bin/sam-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 38%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mem.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 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-I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar.dir/kar.c.o -MF CMakeFiles/kar.dir/kar.c.o.d -o CMakeFiles/kar.dir/kar.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c [ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fastq_iter.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fastq_iter.c.o -MF CMakeFiles/fasterq-dump.dir/fastq_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/fastq_iter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/fastq_iter.c -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s dump-blob-boundaries.3.0.3 dump-blob-boundaries.3 -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s dump-blob-boundaries.3 dump-blob-boundaries -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 39%] Building C object 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target dump-blob-boundaries -[ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/caps.c.o -make -f tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build.make tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/depend cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+print.c.o -MF CMakeFiles/kar+.dir/kar+print.c.o.d -o CMakeFiles/kar+.dir/kar+print.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+print.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/caps.c.o -MF CMakeFiles/sra-sort-cg.dir/caps.c.o.d -o CMakeFiles/sra-sort-cg.dir/caps.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/caps.c -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sam-dump.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sam-dump sam-dump.3.0.3 -[ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/membank.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/membank.c.o -MF CMakeFiles/sra-sort.dir/membank.c.o.d -o CMakeFiles/sra-sort.dir/membank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/membank.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sam-dump.3.0.3 sam-dump.3 -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build.make tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sam-dump.3 sam-dump -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sam-dump-driver +[ 40%] Linking C executable ../../../bin/sra-pileup +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-pileup.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-pileup.dir/dyn_string.c.o" "CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o" "CMakeFiles/sra-pileup.dir/out_redir.c.o" "CMakeFiles/sra-pileup.dir/perf_log.c.o" "CMakeFiles/sra-pileup.dir/reref.c.o" "CMakeFiles/sra-pileup.dir/cg_tools.c.o" "CMakeFiles/sra-pileup.dir/report_deletes.c.o" "CMakeFiles/sra-pileup.dir/ref_regions.c.o" "CMakeFiles/sra-pileup.dir/4na_ascii.c.o" "CMakeFiles/sra-pileup.dir/ref_walker_0.c.o" "CMakeFiles/sra-pileup.dir/ref_walker.c.o" "CMakeFiles/sra-pileup.dir/walk_debug.c.o" "CMakeFiles/sra-pileup.dir/pileup_counters.c.o" "CMakeFiles/sra-pileup.dir/pileup_index.c.o" "CMakeFiles/sra-pileup.dir/pileup_indels.c.o" "CMakeFiles/sra-pileup.dir/pileup_varcount.c.o" "CMakeFiles/sra-pileup.dir/pileup_stat.c.o" "CMakeFiles/sra-pileup.dir/pileup_v2.c.o" "CMakeFiles/sra-pileup.dir/sra-pileup.c.o" -o ../../../bin/sra-pileup /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'cg_canonical_print_cigar': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1579:12: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] + 1579 | return rc; + | ^~ +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1547:10: note: 'rc' was declared here + 1547 | rc_t rc; + | ^~ +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1574:13: warning: 'total_cnt' may be used uninitialized [-Wmaybe-uninitialized] + 1574 | KOutMsg( "%d%c", total_cnt, op ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1549:16: note: 'total_cnt' was declared here + 1549 | int i, total_cnt, cnt; + | ^~~~~~~~~ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-pileup.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-pileup sra-pileup.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-pileup.3.0.3 sra-pileup.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-pileup.3 sra-pileup +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sra-pileup-driver +[ 40%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump.c.o make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 41%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/spot-assembler.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/spot-assembler.c.o -MF CMakeFiles/fastqloader.dir/spot-assembler.c.o.d -o CMakeFiles/fastqloader.dir/spot-assembler.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/spot-assembler.c -[ 41%] Built target sam-dump -make -f tools/loaders/sharq/CMakeFiles/sharq.py.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.py.dir/depend +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump.c.o -MF CMakeFiles/sam-dump.dir/sam-dump.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c +[ 40%] Built target sra-pileup +make -f tools/loaders/kar/CMakeFiles/kar+meta.dir/build.make tools/loaders/kar/CMakeFiles/kar+meta.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq/CMakeFiles/sharq.py.dir/DependInfo.cmake --color= +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar+meta.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/sharq/CMakeFiles/sharq.py.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.py.dir/build +make -f tools/loaders/kar/CMakeFiles/kar+meta.dir/build.make tools/loaders/kar/CMakeFiles/kar+meta.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq && /usr/bin/cmake -E copy /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/sharq.py /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq.py -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mem.c.o +[ 40%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+util.c.o +[ 40%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tbl_join.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tbl_join.c.o -MF CMakeFiles/fasterq-dump.dir/tbl_join.c.o.d -o CMakeFiles/fasterq-dump.dir/tbl_join.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/tbl_join.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+util.c.o -MF CMakeFiles/kar+.dir/kar+util.c.o.d -o CMakeFiles/kar+.dir/kar+util.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+util.c +[ 40%] Building C object tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+util.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+util.c.o -MF CMakeFiles/kar+meta.dir/kar+util.c.o.d -o CMakeFiles/kar+meta.dir/kar+util.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+util.c +In file included from /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:68: +/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp: In lambda function: +/usr/include/ncbi-vdb/klib/debug.h:547:27: warning: statement has no effect [-Wunused-value] + 547 | #define KDbgSetString(s) ((rc_t)0) + | ~^~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:464:13: note: in expansion of macro 'KDbgSetString' + 464 | KDbgSetString(arg.argument); + | ^~~~~~~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'DumpQuality': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:1096:37: warning: the comparison will always evaluate as 'true' for the address of 'qualQuant' will never be NULL [-Waddress] + 1096 | char const newValue = ((param->qualQuant && param->qualQuantSingle)?param->qualQuantSingle:30) + 33; + | ^~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:205:13: note: 'qualQuant' declared here + 205 | uint8_t qualQuant[256]; + | ^~~~~~~~~ +[ 40%] Linking C executable ../../../bin/srapath In function 'kar_persist_karalias', inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1067:14, inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1038:9: @@ -4285,15 +4241,34 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:919:28: note: 'total_written' was declared here 919 | size_t total_expected, total_written; | ^~~~~~~~~~~~~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mem.c.o -MF CMakeFiles/sra-sort-cg.dir/mem.c.o.d -o CMakeFiles/sra-sort-cg.dir/mem.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c -[ 41%] Built target sharq.py -make -f tools/loaders/sra-load/CMakeFiles/sff-load.dir/build.make tools/loaders/sra-load/CMakeFiles/sff-load.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/sff-load.dir/DependInfo.cmake --color= +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cmake -E cmake_link_script CMakeFiles/srapath.dir/link.txt --verbose=1 +[ 40%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_registry.c.o +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'SetupColumns': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:3230:10: warning: the comparison will always evaluate as 'true' for the address of 'qualQuant' will never be NULL [-Waddress] + 3230 | if ( param -> qualQuant && param -> qualQuantSingle ) { /** we don't really need quality ***/ + | ^~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:205:13: note: 'qualQuant' declared here + 205 | uint8_t qualQuant[256]; + | ^~~~~~~~~ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_registry.c.o -MF CMakeFiles/fasterq-dump.dir/temp_registry.c.o.d -o CMakeFiles/fasterq-dump.dir/temp_registry.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/temp_registry.c +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'SAM_Dump_Main': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:4380:22: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 4380 | ReportBuildDate( __DATE__ ); + | ^~~~~~~~ +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/srapath.dir/helper.c.o CMakeFiles/srapath.dir/line_iter.c.o "CMakeFiles/srapath.dir/repository-mgr.c.o" CMakeFiles/srapath.dir/services.c.o CMakeFiles/srapath.dir/cgi_request.c.o CMakeFiles/srapath.dir/srapath.c.o -o ../../../bin/srapath /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f srapath.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv srapath srapath.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srapath.3.0.3 srapath.3 +/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp: At global scope: +/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:390:13: warning: 'void sratools::do_sratools(const CommandLine&)' defined but not used [-Wunused-function] + 390 | static void do_sratools [[noreturn]] (CommandLine const &argv) + | ^~~~~~~~~~~ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srapath.3 srapath /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'ProcessHeaderText': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:690:14: warning: 'value' may be used uninitialized [-Wmaybe-uninitialized] 690 | unsigned value; | ^~~~~ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 srapath-driver In function 'ParseSQ', inlined from 'ParseHeader' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:917:47, inlined from 'ProcessHeaderText' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1063:25: @@ -4305,44 +4280,21 @@ 689 | unsigned tag; | ^~~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/sra-load/CMakeFiles/sff-load.dir/build.make tools/loaders/sra-load/CMakeFiles/sff-load.dir/build +[ 40%] Built target srapath +make -f tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build.make tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/depend +[ 40%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/copy_machine.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/copy_machine.c.o -MF CMakeFiles/fasterq-dump.dir/copy_machine.c.o.d -o CMakeFiles/fasterq-dump.dir/copy_machine.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/copy_machine.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 41%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/pstring.c.o -In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:28: -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] - 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) - | ^~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:33:1: note: in expansion of macro 'FILE_ENTRY' - 33 | FILE_ENTRY ( mem ); - | ^~~~~~~~~~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/pstring.c.o -MF CMakeFiles/sff-load.dir/pstring.c.o.d -o CMakeFiles/sff-load.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c -[ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-membank.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-membank.c.o -MF CMakeFiles/sra-sort.dir/paged-membank.c.o.d -o CMakeFiles/sra-sort.dir/paged-membank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-membank.c -[ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/membank.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/membank.c.o -MF CMakeFiles/sra-sort-cg.dir/membank.c.o.d -o CMakeFiles/sra-sort-cg.dir/membank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/membank.c -[ 41%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+util.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+util.c.o -MF CMakeFiles/kar+.dir/kar+util.c.o.d -o CMakeFiles/kar+.dir/kar+util.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+util.c -[ 41%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tbl_join.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tbl_join.c.o -MF CMakeFiles/fasterq-dump.dir/tbl_join.c.o.d -o CMakeFiles/fasterq-dump.dir/tbl_join.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/tbl_join.c -[ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-mmapbank.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-mmapbank.c.o -MF CMakeFiles/sra-sort.dir/paged-mmapbank.c.o.d -o CMakeFiles/sra-sort.dir/paged-mmapbank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-mmapbank.c -[ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-membank.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-membank.c.o -MF CMakeFiles/sra-sort-cg.dir/paged-membank.c.o.d -o CMakeFiles/sra-sort-cg.dir/paged-membank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-membank.c -[ 42%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/common-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/common-xml.c.o -MF CMakeFiles/sff-load.dir/common-xml.c.o.d -o CMakeFiles/sff-load.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c -[ 42%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-writer.c.o -MF CMakeFiles/fastqloader.dir/common-writer.c.o.d -o CMakeFiles/fastqloader.dir/common-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c -In file included from /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:68: -/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp: In lambda function: -/usr/include/ncbi-vdb/klib/debug.h:547:27: warning: statement has no effect [-Wunused-value] - 547 | #define KDbgSetString(s) ((rc_t)0) - | ~^~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:464:13: note: in expansion of macro 'KDbgSetString' - 464 | KDbgSetString(arg.argument); - | ^~~~~~~~~~~~~ -[ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/except.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/except.c.o -MF CMakeFiles/sra-sort.dir/except.c.o.d -o CMakeFiles/sra-sort.dir/except.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c -[ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build.make tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 40%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+.c.o -MF CMakeFiles/kar+.dir/kar+.c.o.d -o CMakeFiles/kar+.dir/kar+.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c +[ 40%] Building C object tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o -MF CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o.d -o CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/dump-blob-boundaries.c +[ 40%] Linking C executable ../../../bin/dump-blob-boundaries +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cmake -E cmake_link_script CMakeFiles/dump-blob-boundaries.dir/link.txt --verbose=1 /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'ProcessHeaderText': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:690:14: warning: 'value' may be used uninitialized [-Wmaybe-uninitialized] 690 | unsigned value; @@ -4357,16 +4309,25 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:689:14: note: 'tag' was declared here 689 | unsigned tag; | ^~~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o -MF CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o.d -o CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-mmapbank.c -In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:28: -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] - 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) - | ^~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:42:1: note: in expansion of macro 'FILE_ENTRY' - 42 | FILE_ENTRY ( except ); - | ^~~~~~~~~~ -[ 42%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+.c.o -MF CMakeFiles/kar+.dir/kar+.c.o.d -o CMakeFiles/kar+.dir/kar+.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o" -o ../../../bin/dump-blob-boundaries /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 40%] Building C object tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+meta.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+meta.c.o -MF CMakeFiles/kar+meta.dir/kar+meta.c.o.d -o CMakeFiles/kar+meta.dir/kar+meta.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+meta.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f dump-blob-boundaries.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv dump-blob-boundaries dump-blob-boundaries.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s dump-blob-boundaries.3.0.3 dump-blob-boundaries.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s dump-blob-boundaries.3 dump-blob-boundaries +[ 40%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/concatenator.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/concatenator.c.o -MF CMakeFiles/fasterq-dump.dir/concatenator.c.o.d -o CMakeFiles/fasterq-dump.dir/concatenator.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/concatenator.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 40%] Built target dump-blob-boundaries +make -f tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 40%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/caps.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/caps.c.o -MF CMakeFiles/sra-sort.dir/caps.c.o.d -o CMakeFiles/sra-sort.dir/caps.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/caps.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMakeAlignment': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1774:14: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 1774 | if (!BAM_AlignmentInit(y, rsltsize, datasize, &y->extra[numExtra])) @@ -4374,58 +4335,49 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1694:13: note: by argument 4 of type 'const void * const' to 'BAM_AlignmentInit' declared here 1694 | static bool BAM_AlignmentInit(BAM_Alignment *const self, unsigned const maxsize, | ^~~~~~~~~~~~~~~~~ -[ 42%] Linking C executable ../../../bin/kar +[ 40%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o -MF CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o.d -o CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/fasterq-dump.c +In function 'kar_persist_karalias', + inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:761:14, + inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:726:9: +/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:720:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] + 720 | *num_writ = total_written; + | ~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c: In function 'kar_persist': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:676:28: note: 'total_written' was declared here + 676 | size_t total_expected, total_written; + | ^~~~~~~~~~~~~ +In function 'kar_persist_karfile', + inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:748:14, + inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:726:9: +/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:652:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] + 652 | *num_writ = total_written; + | ~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c: In function 'kar_persist': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:607:28: note: 'total_written' was declared here + 607 | size_t total_expected, total_written; + | ^~~~~~~~~~~~~ +[ 40%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mem.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mem.c.o -MF CMakeFiles/sra-sort.dir/mem.c.o.d -o CMakeFiles/sra-sort.dir/mem.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c +[ 40%] Linking C executable ../../../bin/kar cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar.dir/link.txt --verbose=1 -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c: In function 'readThread': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:691:16: warning: pointer 'rslt' may be used after 'free' [-Wuse-after-free] - 691 | if ( rr->type == rr_fileDone ) - | ~~^~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:647:13: note: call to 'free' here - 647 | free(rr); - | ^~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:691:16: warning: pointer 'rslt' may be used after 'free' [-Wuse-after-free] - 691 | if ( rr->type == rr_fileDone ) - | ~~^~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:647:13: note: call to 'free' here - 647 | free(rr); - | ^~~~~~~~ -[ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/idx-mapping.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/idx-mapping.c.o -MF CMakeFiles/sra-sort.dir/idx-mapping.c.o.d -o CMakeFiles/sra-sort.dir/idx-mapping.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/kar.dir/kar-path.c.o" "CMakeFiles/kar.dir/kar-args.c.o" CMakeFiles/kar.dir/kar.c.o -o ../../../bin/kar /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 42%] Linking C executable ../../../bin/kar+meta -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar+meta.dir/link.txt --verbose=1 -[ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/except.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/except.c.o -MF CMakeFiles/sra-sort-cg.dir/except.c.o.d -o CMakeFiles/sra-sort-cg.dir/except.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/kar+meta.dir/kar+util.c.o CMakeFiles/kar+meta.dir/kar+meta.c.o -o ../../../bin/kar+meta /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:28: -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] - 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) - | ^~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:32:1: note: in expansion of macro 'FILE_ENTRY' - 32 | FILE_ENTRY ( idx-mapping ); - | ^~~~~~~~~~ -In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:28: +[ 40%] Building C object tools/external/test-sra/CMakeFiles/test-sra.dir/unix/PrintOS.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/test-sra\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/test-sra/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/test-sra/CMakeFiles/test-sra.dir/unix/PrintOS.c.o -MF CMakeFiles/test-sra.dir/unix/PrintOS.c.o.d -o CMakeFiles/test-sra.dir/unix/PrintOS.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/test-sra/unix/PrintOS.c +In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:28: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:42:1: note: in expansion of macro 'FILE_ENTRY' - 42 | FILE_ENTRY ( except ); +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:33:1: note: in expansion of macro 'FILE_ENTRY' + 33 | FILE_ENTRY ( mem ); | ^~~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp: At global scope: -/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:390:13: warning: 'void sratools::do_sratools(const CommandLine&)' defined but not used [-Wunused-function] - 390 | static void do_sratools [[noreturn]] (CommandLine const &argv) - | ^~~~~~~~~~~ +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/kar.dir/kar-path.c.o" "CMakeFiles/kar.dir/kar-args.c.o" CMakeFiles/kar.dir/kar.c.o -o ../../../bin/kar /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 40%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/membank.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/membank.c.o -MF CMakeFiles/sra-sort.dir/membank.c.o.d -o CMakeFiles/sra-sort.dir/membank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/membank.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kar kar.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar.3.0.3 kar.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar.3 kar -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar+meta.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kar+meta kar+meta.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o -MF CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o.d -o CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+meta.3.0.3 kar+meta.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+meta.3 kar+meta In function 'ProcessBAMHeader', inlined from 'BAM_FileMakeWithKFileAndHeader' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1421:14, inlined from 'BAM_FileMake' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1479:14: @@ -4436,84 +4388,123 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1282:16: note: 'refSeq' was declared here 1282 | BAMRefSeq *refSeq; | ^~~~~~ -[ 42%] Built target kar +[ 40%] Built target kar +make -f tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build.make tools/loaders/sra-load/CMakeFiles/fastq-load.dir/depend +make -f tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build +[ 40%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump3.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump3.c.o -MF CMakeFiles/sam-dump.dir/sam-dump3.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump3.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/fastq-load.dir/DependInfo.cmake --color= -In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:28: +[ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/caps.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/caps.c.o -MF CMakeFiles/sra-sort-cg.dir/caps.c.o.d -o CMakeFiles/sra-sort-cg.dir/caps.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/caps.c +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c: In function 'KMain': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:557:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 557 | ReportBuildDate( __DATE__ ); + | ^~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMakeAlignment': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1774:14: warning: '' may be used uninitialized [-Wmaybe-uninitialized] + 1774 | if (!BAM_AlignmentInit(y, rsltsize, datasize, &y->extra[numExtra])) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1694:13: note: by argument 4 of type 'const void * const' to 'BAM_AlignmentInit' declared here + 1694 | static bool BAM_AlignmentInit(BAM_Alignment *const self, unsigned const maxsize, + | ^~~~~~~~~~~~~~~~~ +In function 'samdump_main', + inlined from 'KMain' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:558:26: +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:510:10: warning: 'mode' may be used uninitialized [-Wmaybe-uninitialized] + 510 | rc = init_out_redir( &redir, mode, opts->outputfile, opts->output_buffer_size ); /* from out_redir.c */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c: In function 'KMain': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:502:25: note: 'mode' was declared here + 502 | enum out_redir_mode mode; + | ^~~~ +[ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-membank.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-membank.c.o -MF CMakeFiles/sra-sort.dir/paged-membank.c.o.d -o CMakeFiles/sra-sort.dir/paged-membank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-membank.c +[ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mem.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mem.c.o -MF CMakeFiles/sra-sort-cg.dir/mem.c.o.d -o CMakeFiles/sra-sort-cg.dir/mem.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c +[ 41%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/dyn_string.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/dyn_string.c.o -MF CMakeFiles/sam-dump.dir/dyn_string.c.o.d -o CMakeFiles/sam-dump.dir/dyn_string.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/dyn_string.c +[ 41%] Linking C executable ../../../bin/test-sra +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sra.dir/link.txt --verbose=1 +In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:28: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:32:1: note: in expansion of macro 'FILE_ENTRY' - 32 | FILE_ENTRY ( idx-mapping ); +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:33:1: note: in expansion of macro 'FILE_ENTRY' + 33 | FILE_ENTRY ( mem ); | ^~~~~~~~~~ -[ 42%] Built target kar+meta +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sra.dir/test-sra.c.o" "CMakeFiles/test-sra.dir/unix/PrintOS.c.o" -o ../../../bin/test-sra ../../../ilib/libascp.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +make -f tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build.make tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/DependInfo.cmake --color= +[ 42%] Linking C executable ../../../bin/vdb-dump +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-dump.dir/link.txt --verbose=1 +[ 42%] Linking C executable ../../../bin/fasterq-dump +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/fasterq-dump.dir/link.txt --verbose=1 +[ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/membank.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/membank.c.o -MF CMakeFiles/sra-sort-cg.dir/membank.c.o.d -o CMakeFiles/sra-sort-cg.dir/membank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/membank.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build.make tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build +make -f tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build.make tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/sra-load/CMakeFiles/srf-load.dir/build.make tools/loaders/sra-load/CMakeFiles/srf-load.dir/depend +[ 42%] Linking C executable ../../../bin/kar+meta +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar+meta.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/fasterq-dump.dir/helper.c.o" "CMakeFiles/fasterq-dump.dir/arg_helper.c.o" "CMakeFiles/fasterq-dump.dir/dflt_defline.c.o" "CMakeFiles/fasterq-dump.dir/tool_ctx.c.o" "CMakeFiles/fasterq-dump.dir/inspector.c.o" "CMakeFiles/fasterq-dump.dir/sbuffer.c.o" "CMakeFiles/fasterq-dump.dir/err_msg.c.o" "CMakeFiles/fasterq-dump.dir/file_tools.c.o" "CMakeFiles/fasterq-dump.dir/var_fmt.c.o" "CMakeFiles/fasterq-dump.dir/flex_printer.c.o" "CMakeFiles/fasterq-dump.dir/temp_dir.c.o" "CMakeFiles/fasterq-dump.dir/progress_thread.c.o" "CMakeFiles/fasterq-dump.dir/cleanup_task.c.o" "CMakeFiles/fasterq-dump.dir/index.c.o" "CMakeFiles/fasterq-dump.dir/lookup_writer.c.o" "CMakeFiles/fasterq-dump.dir/lookup_reader.c.o" "CMakeFiles/fasterq-dump.dir/locked_file_list.c.o" "CMakeFiles/fasterq-dump.dir/locked_value.c.o" "CMakeFiles/fasterq-dump.dir/file_printer.c.o" "CMakeFiles/fasterq-dump.dir/merge_sorter.c.o" "CMakeFiles/fasterq-dump.dir/sorter.c.o" "CMakeFiles/fasterq-dump.dir/cmn_iter.c.o" "CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o" "CMakeFiles/fasterq-dump.dir/special_iter.c.o" "CMakeFiles/fasterq-dump.dir/fastq_iter.c.o" "CMakeFiles/fasterq-dump.dir/db_join.c.o" "CMakeFiles/fasterq-dump.dir/tbl_join.c.o" "CMakeFiles/fasterq-dump.dir/temp_registry.c.o" "CMakeFiles/fasterq-dump.dir/copy_machine.c.o" "CMakeFiles/fasterq-dump.dir/concatenator.c.o" "CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o" -o ../../../bin/fasterq-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 42%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/spot-assembler.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/spot-assembler.c.o -MF CMakeFiles/fastqloader.dir/spot-assembler.c.o.d -o CMakeFiles/fastqloader.dir/spot-assembler.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/spot-assembler.c +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/kar+meta.dir/kar+util.c.o CMakeFiles/kar+meta.dir/kar+meta.c.o -o ../../../bin/kar+meta /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o" "CMakeFiles/vdb-dump.dir/vdb_info.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump.c.o" -o ../../../bin/vdb-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-sra.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv test-sra test-sra.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-sra.3.0.3 test-sra.3 +[ 42%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-sra.3 test-sra +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-writer.c.o -MF CMakeFiles/fastqloader.dir/common-writer.c.o.d -o CMakeFiles/fastqloader.dir/common-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 42%] Built target test-sra +make -f tools/loaders/sharq/CMakeFiles/sharq.py.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.py.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/map-file.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/srf-load.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/map-file.c.o -MF CMakeFiles/sra-sort.dir/map-file.c.o.d -o CMakeFiles/sra-sort.dir/map-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/map-file.c -[ 42%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/pstring.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/pstring.c.o -MF CMakeFiles/fastq-load.dir/pstring.c.o.d -o CMakeFiles/fastq-load.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq/CMakeFiles/sharq.py.dir/DependInfo.cmake --color= +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-dump.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-dump vdb-dump.3.0.3 +[ 43%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-mmapbank.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar+meta.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-mmapbank.c.o -MF CMakeFiles/sra-sort.dir/paged-mmapbank.c.o.d -o CMakeFiles/sra-sort.dir/paged-mmapbank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-mmapbank.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-dump.3.0.3 vdb-dump.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kar+meta kar+meta.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+meta.3.0.3 kar+meta.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-dump.3 vdb-dump +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+meta.3 kar+meta +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/loaders/sharq/CMakeFiles/sharq.py.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.py.dir/build +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 vdb-dump-driver make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/sra-load/CMakeFiles/srf-load.dir/build.make tools/loaders/sra-load/CMakeFiles/srf-load.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -In function 'kar_persist_karalias', - inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:761:14, - inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:726:9: -/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:720:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] - 720 | *num_writ = total_written; - | ~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c: In function 'kar_persist': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:676:28: note: 'total_written' was declared here - 676 | size_t total_expected, total_written; - | ^~~~~~~~~~~~~ -In function 'kar_persist_karfile', - inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:748:14, - inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:726:9: -/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:652:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] - 652 | *num_writ = total_written; - | ~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c: In function 'kar_persist': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:607:28: note: 'total_written' was declared here - 607 | size_t total_expected, total_written; - | ^~~~~~~~~~~~~ -[ 42%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/pstring.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/pstring.c.o -MF CMakeFiles/srf-load.dir/pstring.c.o.d -o CMakeFiles/srf-load.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c -[ 42%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_registry.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_registry.c.o -MF CMakeFiles/fasterq-dump.dir/temp_registry.c.o.d -o CMakeFiles/fasterq-dump.dir/temp_registry.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/temp_registry.c -/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMakeAlignment': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1774:14: warning: '' may be used uninitialized [-Wmaybe-uninitialized] - 1774 | if (!BAM_AlignmentInit(y, rsltsize, datasize, &y->extra[numExtra])) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1694:13: note: by argument 4 of type 'const void * const' to 'BAM_AlignmentInit' declared here - 1694 | static bool BAM_AlignmentInit(BAM_Alignment *const self, unsigned const maxsize, - | ^~~~~~~~~~~~~~~~~ -[ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/map-file.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/map-file.c.o -MF CMakeFiles/sra-sort-cg.dir/map-file.c.o.d -o CMakeFiles/sra-sort-cg.dir/map-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/map-file.c -[ 42%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/copy_machine.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/copy_machine.c.o -MF CMakeFiles/fasterq-dump.dir/copy_machine.c.o.d -o CMakeFiles/fasterq-dump.dir/copy_machine.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/copy_machine.c -[ 42%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/experiment-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/experiment-xml.c.o -MF CMakeFiles/sff-load.dir/experiment-xml.c.o.d -o CMakeFiles/sff-load.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c -[ 42%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/common-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/common-xml.c.o -MF CMakeFiles/fastq-load.dir/common-xml.c.o.d -o CMakeFiles/fastq-load.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c -[ 42%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/sequence-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/sequence-writer.c.o -MF CMakeFiles/fastqloader.dir/sequence-writer.c.o.d -o CMakeFiles/fastqloader.dir/sequence-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/sequence-writer.c -[ 42%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/concatenator.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/concatenator.c.o -MF CMakeFiles/fasterq-dump.dir/concatenator.c.o.d -o CMakeFiles/fasterq-dump.dir/concatenator.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/concatenator.c -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] - 711 | const char* b = NULL; - | ^ -[ 42%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/common-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/common-xml.c.o -MF CMakeFiles/srf-load.dir/common-xml.c.o.d -o CMakeFiles/srf-load.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq && /usr/bin/cmake -E copy /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/sharq.py /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq.py +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 43%] Built target kar+meta +make -f tools/loaders/sra-load/CMakeFiles/sff-load.dir/build.make tools/loaders/sra-load/CMakeFiles/sff-load.dir/depend +[ 43%] Built target vdb-dump +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/sff-load.dir/DependInfo.cmake --color= +make -f tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build.make tools/loaders/sra-load/CMakeFiles/fastq-load.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/fastq-load.dir/DependInfo.cmake --color= +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fasterq-dump.3.0.3 +[ 43%] Built target sharq.py +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fasterq-dump fasterq-dump.3.0.3 +make -f tools/loaders/sra-load/CMakeFiles/srf-load.dir/build.make tools/loaders/sra-load/CMakeFiles/srf-load.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In function 'ProcessBAMHeader', inlined from 'BAM_FileMakeWithKFileAndHeader' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1421:14, inlined from 'BAM_FileMake' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1479:14: +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fasterq-dump.3.0.3 fasterq-dump.3 +[ 43%] Linking C executable ../../../bin/kar+ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar+.dir/link.txt --verbose=1 +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/srf-load.dir/DependInfo.cmake --color= +make -f tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build.make tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1321:18: warning: 'refSeq' may be used uninitialized [-Wmaybe-uninitialized] 1321 | self->refSeq = refSeq; | ~~~~~~~~~~~~~^~~~~~~~ @@ -4521,155 +4512,185 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1282:16: note: 'refSeq' was declared here 1282 | BAMRefSeq *refSeq; | ^~~~~~ -[ 42%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o -MF CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o.d -o CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/fasterq-dump.c -[ 42%] Linking C executable ../../../bin/kar+ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar+.dir/link.txt --verbose=1 +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fasterq-dump.3 fasterq-dump +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 fasterq-dump-driver +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 43%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-membank.c.o +make -f tools/loaders/sra-load/CMakeFiles/sff-load.dir/build.make tools/loaders/sra-load/CMakeFiles/sff-load.dir/build +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-membank.c.o -MF CMakeFiles/sra-sort-cg.dir/paged-membank.c.o.d -o CMakeFiles/sra-sort-cg.dir/paged-membank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-membank.c +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/kar+.dir/kar-path.c.o" CMakeFiles/kar+.dir/kar+args.c.o CMakeFiles/kar+.dir/kar+print.c.o CMakeFiles/kar+.dir/kar+util.c.o CMakeFiles/kar+.dir/kar+.c.o -o ../../../bin/kar+ /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/col-pair.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/col-pair.c.o -MF CMakeFiles/sra-sort.dir/col-pair.c.o.d -o CMakeFiles/sra-sort.dir/col-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/col-pair.c -[ 42%] Building C object tools/external/test-sra/CMakeFiles/test-sra.dir/unix/PrintOS.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/test-sra\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/test-sra/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/test-sra/CMakeFiles/test-sra.dir/unix/PrintOS.c.o -MF CMakeFiles/test-sra.dir/unix/PrintOS.c.o.d -o CMakeFiles/test-sra.dir/unix/PrintOS.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/test-sra/unix/PrintOS.c -[ 42%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-str.c -[ 42%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-reader.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-reader.c.o -MF CMakeFiles/fastqloader.dir/common-reader.c.o.d -o CMakeFiles/fastqloader.dir/common-reader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-reader.c -[ 42%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/fastq-reader.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/fastq-reader.c.o -MF CMakeFiles/fastqloader.dir/fastq-reader.c.o.d -o CMakeFiles/fastqloader.dir/fastq-reader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-reader.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar+.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kar+ kar+.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+.3.0.3 kar+.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+.3 kar+ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 42%] Built target kar+ +make -f tools/loaders/sra-load/CMakeFiles/srf-load.dir/build.make tools/loaders/sra-load/CMakeFiles/srf-load.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 43%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/pstring.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/pstring.c.o -MF CMakeFiles/fastq-load.dir/pstring.c.o.d -o CMakeFiles/fastq-load.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c +[ 43%] Built target fasterq-dump +[ 43%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/pstring.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/pstring.c.o -MF CMakeFiles/sff-load.dir/pstring.c.o.d -o CMakeFiles/sff-load.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c make -f tools/loaders/sra-load/CMakeFiles/abi-load.dir/build.make tools/loaders/sra-load/CMakeFiles/abi-load.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/abi-load.dir/DependInfo.cmake --color= -[ 42%] Linking C executable ../../../bin/test-sra -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sra.dir/link.txt --verbose=1 +[ 43%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/pstring.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/pstring.c.o -MF CMakeFiles/srf-load.dir/pstring.c.o.d -o CMakeFiles/srf-load.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/abi-load.dir/build.make tools/loaders/sra-load/CMakeFiles/abi-load.dir/build -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sra.dir/test-sra.c.o" "CMakeFiles/test-sra.dir/unix/PrintOS.c.o" -o ../../../bin/test-sra ../../../ilib/libascp.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 42%] Linking C executable ../../../bin/fasterq-dump -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/fasterq-dump.dir/link.txt --verbose=1 -[ 42%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/pstring.c.o +[ 43%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/pstring.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/pstring.c.o -MF CMakeFiles/abi-load.dir/pstring.c.o.d -o CMakeFiles/abi-load.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/fasterq-dump.dir/helper.c.o" "CMakeFiles/fasterq-dump.dir/arg_helper.c.o" "CMakeFiles/fasterq-dump.dir/dflt_defline.c.o" "CMakeFiles/fasterq-dump.dir/tool_ctx.c.o" "CMakeFiles/fasterq-dump.dir/inspector.c.o" "CMakeFiles/fasterq-dump.dir/sbuffer.c.o" "CMakeFiles/fasterq-dump.dir/err_msg.c.o" "CMakeFiles/fasterq-dump.dir/file_tools.c.o" "CMakeFiles/fasterq-dump.dir/var_fmt.c.o" "CMakeFiles/fasterq-dump.dir/flex_printer.c.o" "CMakeFiles/fasterq-dump.dir/temp_dir.c.o" "CMakeFiles/fasterq-dump.dir/progress_thread.c.o" "CMakeFiles/fasterq-dump.dir/cleanup_task.c.o" "CMakeFiles/fasterq-dump.dir/index.c.o" "CMakeFiles/fasterq-dump.dir/lookup_writer.c.o" "CMakeFiles/fasterq-dump.dir/lookup_reader.c.o" "CMakeFiles/fasterq-dump.dir/locked_file_list.c.o" "CMakeFiles/fasterq-dump.dir/locked_value.c.o" "CMakeFiles/fasterq-dump.dir/file_printer.c.o" "CMakeFiles/fasterq-dump.dir/merge_sorter.c.o" "CMakeFiles/fasterq-dump.dir/sorter.c.o" "CMakeFiles/fasterq-dump.dir/cmn_iter.c.o" "CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o" "CMakeFiles/fasterq-dump.dir/special_iter.c.o" "CMakeFiles/fasterq-dump.dir/fastq_iter.c.o" "CMakeFiles/fasterq-dump.dir/db_join.c.o" "CMakeFiles/fasterq-dump.dir/tbl_join.c.o" "CMakeFiles/fasterq-dump.dir/temp_registry.c.o" "CMakeFiles/fasterq-dump.dir/copy_machine.c.o" "CMakeFiles/fasterq-dump.dir/concatenator.c.o" "CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o" -o ../../../bin/fasterq-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 43%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/sam.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/sam.c.o -MF CMakeFiles/samview.dir/sam.c.o.d -o CMakeFiles/samview.dir/sam.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sam.c -[ 44%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/col-pair.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/col-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/col-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/col-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/col-pair.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-sra.3.0.3 -[ 44%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-helper.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv test-sra test-sra.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-sra.3.0.3 test-sra.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-sra.3 test-sra +[ 43%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/except.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/except.c.o -MF CMakeFiles/sra-sort.dir/except.c.o.d -o CMakeFiles/sra-sort.dir/except.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar+.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kar+ kar+.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+.3.0.3 kar+.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+.3 kar+ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fasterq-dump.3.0.3 -[ 44%] Built target test-sra +In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:28: +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] + 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) + | ^~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:42:1: note: in expansion of macro 'FILE_ENTRY' + 42 | FILE_ENTRY ( except ); + | ^~~~~~~~~~ +[ 43%] Built target kar+ make -f tools/loaders/sra-load/CMakeFiles/illumina-load.dir/build.make tools/loaders/sra-load/CMakeFiles/illumina-load.dir/depend -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fasterq-dump fasterq-dump.3.0.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/illumina-load.dir/DependInfo.cmake --color= -make -f tools/loaders/sra-load/CMakeFiles/helicos-load.dir/build.make tools/loaders/sra-load/CMakeFiles/helicos-load.dir/depend -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fasterq-dump.3.0.3 fasterq-dump.3 -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/helicos-load.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fasterq-dump.3 fasterq-dump -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 fasterq-dump-driver -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c: In function 'readThread': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:691:16: warning: pointer 'rslt' may be used after 'free' [-Wuse-after-free] + 691 | if ( rr->type == rr_fileDone ) + | ~~^~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:647:13: note: call to 'free' here + 647 | free(rr); + | ^~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:691:16: warning: pointer 'rslt' may be used after 'free' [-Wuse-after-free] + 691 | if ( rr->type == rr_fileDone ) + | ~~^~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:647:13: note: call to 'free' here + 647 | free(rr); + | ^~~~~~~~ make -f tools/loaders/sra-load/CMakeFiles/illumina-load.dir/build.make tools/loaders/sra-load/CMakeFiles/illumina-load.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 43%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o +[ 44%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/pstring.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time 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CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o.d -o CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-mmapbank.c +[ 44%] Linking C executable ../../../bin/sra-stat +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-stat.dir/link.txt --verbose=1 +[ 44%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/common-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/common-xml.c.o -MF CMakeFiles/fastq-load.dir/common-xml.c.o.d -o CMakeFiles/fastq-load.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-stat.dir/assembly-statistics.c.o" "CMakeFiles/sra-stat.dir/sra.c.o" "CMakeFiles/sra-stat.dir/sra-stat.c.o" -o ../../../bin/sra-stat ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'DumpCGSAM.part.0': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:2455:32: warning: 'last_cig_op' may be used uninitialized [-Wmaybe-uninitialized] + 2455 | if( last_cig_oplen > 0 && last_cig_op == OP){ \ + | ^~ +[ 44%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/idx-mapping.c.o +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:2445:14: note: 'last_cig_op' was declared here + 2445 | char last_cig_op; + | ^~~~~~~~~~~ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/idx-mapping.c.o -MF CMakeFiles/sra-sort.dir/idx-mapping.c.o.d -o CMakeFiles/sra-sort.dir/idx-mapping.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c +[ 44%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/common-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/common-xml.c.o -MF CMakeFiles/sff-load.dir/common-xml.c.o.d -o CMakeFiles/sff-load.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c +[ 44%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/sequence-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/sequence-writer.c.o -MF CMakeFiles/fastqloader.dir/sequence-writer.c.o.d -o 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/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c +[ 44%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/common-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/common-xml.c.o -MF CMakeFiles/abi-load.dir/common-xml.c.o.d -o CMakeFiles/abi-load.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c +In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:28: +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] + 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) + | ^~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:32:1: note: in expansion of macro 'FILE_ENTRY' + 32 | FILE_ENTRY ( idx-mapping ); + | ^~~~~~~~~~ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-stat.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-stat sra-stat.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-stat.3.0.3 sra-stat.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-stat.3 sra-stat make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 44%] Built target sra-stat +make -f tools/loaders/sra-load/CMakeFiles/helicos-load.dir/build.make tools/loaders/sra-load/CMakeFiles/helicos-load.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/helicos-load.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/helicos-load.dir/build.make tools/loaders/sra-load/CMakeFiles/helicos-load.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 44%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/row-set.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/row-set.c.o -MF CMakeFiles/sra-sort.dir/row-set.c.o.d -o CMakeFiles/sra-sort.dir/row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/row-set.c -[ 44%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o -MF CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o.d -o CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-grammar.c -[ 44%] Built target fasterq-dump -make -f tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/build.make tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd 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-I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/pstring.c.o -MF CMakeFiles/helicos-load.dir/pstring.c.o.d -o CMakeFiles/helicos-load.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time 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tools/loaders/sra-load/CMakeFiles/abi-load.dir/common-xml.c.o -MF CMakeFiles/abi-load.dir/common-xml.c.o.d -o CMakeFiles/abi-load.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/build.make tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 45%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pstring.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pstring.c.o -MF CMakeFiles/pacbio-loadxml.dir/pstring.c.o.d -o CMakeFiles/pacbio-loadxml.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c -[ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/simple-row-set.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/simple-row-set.c.o -MF CMakeFiles/sra-sort.dir/simple-row-set.c.o.d -o CMakeFiles/sra-sort.dir/simple-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/simple-row-set.c -[ 45%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/experiment-xml.c.o +[ 44%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/except.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/except.c.o -MF CMakeFiles/sra-sort-cg.dir/except.c.o.d -o CMakeFiles/sra-sort-cg.dir/except.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c +[ 44%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/common-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/common-xml.c.o -MF CMakeFiles/illumina-load.dir/common-xml.c.o.d -o CMakeFiles/illumina-load.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c +In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:28: +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] + 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) + | ^~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:42:1: note: in expansion of macro 'FILE_ENTRY' + 42 | FILE_ENTRY ( except ); + | ^~~~~~~~~~ +[ 45%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/sam.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/sam.c.o -MF CMakeFiles/samview.dir/sam.c.o.d -o CMakeFiles/samview.dir/sam.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sam.c +[ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/map-file.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/map-file.c.o -MF CMakeFiles/sra-sort.dir/map-file.c.o.d -o CMakeFiles/sra-sort.dir/map-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/map-file.c +[ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o -MF CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o.d -o CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c +[ 45%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-reader.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-reader.c.o -MF CMakeFiles/fastqloader.dir/common-reader.c.o.d -o CMakeFiles/fastqloader.dir/common-reader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-reader.c [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/common-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/experiment-xml.c.o -MF CMakeFiles/fastq-load.dir/experiment-xml.c.o.d -o CMakeFiles/fastq-load.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/common-xml.c.o -MF CMakeFiles/helicos-load.dir/common-xml.c.o.d -o CMakeFiles/helicos-load.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c -[ 45%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/run-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/run-xml.c.o -MF CMakeFiles/sff-load.dir/run-xml.c.o.d -o CMakeFiles/sff-load.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c +In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:28: +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] + 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) + | ^~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:32:1: note: in expansion of macro 'FILE_ENTRY' + 32 | FILE_ENTRY ( idx-mapping ); + | ^~~~~~~~~~ +[ 45%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/experiment-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/experiment-xml.c.o -MF CMakeFiles/abi-load.dir/experiment-xml.c.o.d -o CMakeFiles/abi-load.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c [ 45%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sam.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sam.c.o -MF CMakeFiles/bam-load.dir/sam.c.o.d -o CMakeFiles/bam-load.dir/sam.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sam.c +[ 45%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/experiment-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/experiment-xml.c.o -MF CMakeFiles/fastq-load.dir/experiment-xml.c.o.d -o CMakeFiles/fastq-load.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ -[ 45%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/common-xml.c.o -[ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/row-set.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/row-set.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/common-xml.c.o -MF CMakeFiles/illumina-load.dir/common-xml.c.o.d -o CMakeFiles/illumina-load.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c -[ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mapping-row-set.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mapping-row-set.c.o -MF CMakeFiles/sra-sort.dir/mapping-row-set.c.o.d -o CMakeFiles/sra-sort.dir/mapping-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mapping-row-set.c -[ 45%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/experiment-xml.c.o +[ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/map-file.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/map-file.c.o -MF CMakeFiles/sra-sort-cg.dir/map-file.c.o.d -o CMakeFiles/sra-sort-cg.dir/map-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/map-file.c +[ 45%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/fastq-reader.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/fastq-reader.c.o -MF CMakeFiles/fastqloader.dir/fastq-reader.c.o.d -o CMakeFiles/fastqloader.dir/fastq-reader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-reader.c +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] + 711 | const char* b = NULL; + | ^ +[ 45%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o -MF CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o.d -o CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-grammar.c +[ 45%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/experiment-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/experiment-xml.c.o -MF CMakeFiles/illumina-load.dir/experiment-xml.c.o.d -o CMakeFiles/illumina-load.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c +[ 45%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/experiment-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/experiment-xml.c.o -MF CMakeFiles/sff-load.dir/experiment-xml.c.o.d -o CMakeFiles/sff-load.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c +[ 46%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/config.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/config.cpp.o -MF CMakeFiles/sratools.dir/config.cpp.o.d -o CMakeFiles/sratools.dir/config.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/config.cpp +[ 46%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/experiment-xml.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/experiment-xml.c.o -MF CMakeFiles/srf-load.dir/experiment-xml.c.o.d -o CMakeFiles/srf-load.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c -[ 45%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/common-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/common-xml.c.o -MF CMakeFiles/pacbio-loadxml.dir/common-xml.c.o.d -o CMakeFiles/pacbio-loadxml.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ -[ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/simple-row-set.c -[ 45%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-formats.c -[ 45%] Linking C executable ../../../bin/sra-stat -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-stat.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-stat.dir/assembly-statistics.c.o" "CMakeFiles/sra-stat.dir/sra.c.o" "CMakeFiles/sra-stat.dir/sra-stat.c.o" -o ../../../bin/sra-stat ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mapping-row-set.c -[ 46%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sorting-row-set.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sorting-row-set.c.o -MF CMakeFiles/sra-sort.dir/sorting-row-set.c.o.d -o CMakeFiles/sra-sort.dir/sorting-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sorting-row-set.c -[ 46%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/experiment-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/experiment-xml.c.o -MF CMakeFiles/abi-load.dir/experiment-xml.c.o.d -o CMakeFiles/abi-load.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c -[ 46%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-stat.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-redir.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-stat sra-stat.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-stat.3.0.3 sra-stat.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-stat.3 sra-stat -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 46%] Built target sra-stat -make -f tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build.make tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/DependInfo.cmake --color= [ 47%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o -MF CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o.d -o CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build.make tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 47%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/samview.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/samview.c.o -MF CMakeFiles/samview.dir/samview.c.o.d -o CMakeFiles/samview.dir/samview.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/samview.c -[ 47%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o -MF CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o.d -o CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/hdf5/hdf5arrayfile.c +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] + 711 | const char* b = NULL; + | ^ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:750: warning: "YY_BUF_SIZE" redefined 750 | #define YY_BUF_SIZE 16777216 | @@ -4687,8 +4708,6 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1120:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1120 | if ( ! yyg->yy_start ) | ^~ -[ 47%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/meta-pair.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/meta-pair.c.o -MF CMakeFiles/sra-sort.dir/meta-pair.c.o.d -o CMakeFiles/sra-sort.dir/meta-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/meta-pair.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: At top level: /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2409:24: warning: 'yy_fatal_error' defined but not used [-Wunused-function] 2409 | static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner) @@ -4699,286 +4718,358 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1837:16: warning: 'input' defined but not used [-Wunused-function] 1837 | static int input (yyscan_t yyscanner) | ^~~~~ -[ 47%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/run-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/run-xml.c.o -MF CMakeFiles/fastq-load.dir/run-xml.c.o.d -o CMakeFiles/fastq-load.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c -[ 47%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o -[ 47%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-file.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-file.c.o -MF CMakeFiles/sff-load.dir/loader-file.c.o.d -o CMakeFiles/sff-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-fastq.c -[ 47%] Linking C executable ../../../bin/samview -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/samview.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/samview.dir/bam.c.o CMakeFiles/samview.dir/sam.c.o CMakeFiles/samview.dir/samview.c.o -o ../../../bin/samview /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -lz -[ 47%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o -MF 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CMakeFiles/sra-sort.dir/col-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/col-pair.c [ 47%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/experiment-xml.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/experiment-xml.c.o -MF CMakeFiles/helicos-load.dir/experiment-xml.c.o.d -o CMakeFiles/helicos-load.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c -[ 48%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-fmt.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-fmt.c.o -MF CMakeFiles/sff-load.dir/loader-fmt.c.o.d -o CMakeFiles/sff-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c -[ 48%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/dir-pair.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/dir-pair.c.o -MF CMakeFiles/sra-sort.dir/dir-pair.c.o.d -o CMakeFiles/sra-sort.dir/dir-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/dir-pair.c +[ 48%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/col-pair.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/col-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/col-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/col-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/col-pair.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ -[ 48%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/experiment-xml.c.o +[ 48%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/id2name.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/id2name.c.o -MF CMakeFiles/fastqloader.dir/id2name.c.o.d -o CMakeFiles/fastqloader.dir/id2name.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/id2name.c +[ 48%] Linking C executable ../../../bin/sam-dump +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam-dump.dir/link.txt --verbose=1 +[ 48%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/run-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. 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"CMakeFiles/sam-dump.dir/md_flag.c.o" "CMakeFiles/sam-dump.dir/cg_tools.c.o" "CMakeFiles/sam-dump.dir/sam-dump.c.o" "CMakeFiles/sam-dump.dir/sam-dump3.c.o" "CMakeFiles/sam-dump.dir/dyn_string.c.o" -o ../../../bin/sam-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 48%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/samview.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/samview.c.o -MF CMakeFiles/samview.dir/samview.c.o.d -o CMakeFiles/samview.dir/samview.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/samview.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sam-dump.3.0.3 +[ 48%] Linking C executable ../../../bin/samview +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sam-dump sam-dump.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/samview.dir/link.txt --verbose=1 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sam-dump.3.0.3 sam-dump.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sam-dump.3 sam-dump +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sam-dump-driver +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 48%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/run-xml.c.o +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/samview.dir/bam.c.o CMakeFiles/samview.dir/sam.c.o CMakeFiles/samview.dir/samview.c.o -o ../../../bin/samview /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -lz +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/run-xml.c.o -MF CMakeFiles/fastq-load.dir/run-xml.c.o.d -o CMakeFiles/fastq-load.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c +[ 48%] Built target sam-dump +make -f tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/build.make tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load 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tools/loaders/sra-load/CMakeFiles/srf-load.dir/run-xml.c.o -MF CMakeFiles/srf-load.dir/run-xml.c.o.d -o CMakeFiles/srf-load.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c +[ 48%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/row-set.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/row-set.c.o -MF CMakeFiles/sra-sort.dir/row-set.c.o.d -o CMakeFiles/sra-sort.dir/row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/row-set.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv samview samview.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview.3.0.3 samview.3 -[ 49%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/sra-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/sra-writer.c.o -MF CMakeFiles/sff-load.dir/sra-writer.c.o.d -o CMakeFiles/sff-load.dir/sra-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview.3 samview -[ 49%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o -MF CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o.d -o CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c -[ 49%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/meta-pair.c.o -[ 49%] Built target samview -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/meta-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/meta-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/meta-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/meta-pair.c -make -f tools/loaders/cg-load/CMakeFiles/cg-load.dir/build.make tools/loaders/cg-load/CMakeFiles/cg-load.dir/depend +[ 48%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/run-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/run-xml.c.o -MF CMakeFiles/abi-load.dir/run-xml.c.o.d -o CMakeFiles/abi-load.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c +[ 48%] Built target samview +make -f tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build.make tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build.make tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 48%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat 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tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/row-set.c +[ 49%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/run-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/run-xml.c.o -MF CMakeFiles/sff-load.dir/run-xml.c.o.d -o CMakeFiles/sff-load.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c +[ 49%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/simple-row-set.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/simple-row-set.c.o -MF CMakeFiles/sra-sort.dir/simple-row-set.c.o.d -o CMakeFiles/sra-sort.dir/simple-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/simple-row-set.c +[ 49%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/common-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/common-xml.c.o -MF CMakeFiles/pacbio-loadxml.dir/common-xml.c.o.d -o CMakeFiles/pacbio-loadxml.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c +[ 49%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/simple-row-set.c +[ 49%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/run-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/run-xml.c.o -MF CMakeFiles/illumina-load.dir/run-xml.c.o.d -o CMakeFiles/illumina-load.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 50%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/alignment-writer.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/alignment-writer.c.o -MF CMakeFiles/bam-load.dir/alignment-writer.c.o.d -o CMakeFiles/bam-load.dir/alignment-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/alignment-writer.c +[ 50%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mapping-row-set.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mapping-row-set.c.o -MF CMakeFiles/sra-sort.dir/mapping-row-set.c.o.d -o CMakeFiles/sra-sort.dir/mapping-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mapping-row-set.c +[ 50%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mapping-row-set.c +[ 51%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-file.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-file.c.o -MF CMakeFiles/helicos-load.dir/loader-file.c.o.d -o CMakeFiles/helicos-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c +[ 52%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-file.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-file.c.o -MF CMakeFiles/fastq-load.dir/loader-file.c.o.d -o CMakeFiles/fastq-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c +[ 52%] Linking C static library ../../../ilib/libfastqloader.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -P CMakeFiles/fastqloader.dir/cmake_clean_target.cmake +[ 52%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastqloader.dir/link.txt --verbose=1 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 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tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-fmt.c.o -MF CMakeFiles/helicos-load.dir/loader-fmt.c.o.d -o CMakeFiles/helicos-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c +/usr/bin/ar qc ../../../ilib/libfastqloader.a "CMakeFiles/fastqloader.dir/spot-assembler.c.o" "CMakeFiles/fastqloader.dir/common-writer.c.o" "CMakeFiles/fastqloader.dir/sequence-writer.c.o" "CMakeFiles/fastqloader.dir/common-reader.c.o" "CMakeFiles/fastqloader.dir/fastq-reader.c.o" "CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o" "CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o" CMakeFiles/fastqloader.dir/id2name.c.o +/usr/bin/ranlib ../../../ilib/libfastqloader.a +[ 52%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-file.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-file.c.o -MF CMakeFiles/abi-load.dir/loader-file.c.o.d -o CMakeFiles/abi-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 53%] Built target fastqloader +make -f tools/loaders/cg-load/CMakeFiles/cg-load.dir/build.make tools/loaders/cg-load/CMakeFiles/cg-load.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load/CMakeFiles/cg-load.dir/DependInfo.cmake --color= -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] - 711 | const char* b = NULL; - | ^ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/cg-load/CMakeFiles/cg-load.dir/build.make tools/loaders/cg-load/CMakeFiles/cg-load.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] - 711 | const char* b = NULL; - | ^ -[ 50%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/cg-load.c.o +[ 53%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/cg-load.c.o +[ 53%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/sra-writer.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time 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tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-file.c.o -MF CMakeFiles/fastq-load.dir/loader-file.c.o.d -o CMakeFiles/fastq-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c -[ 51%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/tbl-pair.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/tbl-pair.c.o -MF 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tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-fmt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-fmt.c.o -MF CMakeFiles/fastq-load.dir/loader-fmt.c.o.d -o CMakeFiles/fastq-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c +[ 53%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sorting-row-set.c +[ 53%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader.c.o -MF CMakeFiles/helicos-load.dir/loader.c.o.d -o CMakeFiles/helicos-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c +[ 53%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-fmt.c.o +[ 53%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/reference-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-fmt.c.o -MF CMakeFiles/abi-load.dir/loader-fmt.c.o.d -o CMakeFiles/abi-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/reference-writer.c.o -MF CMakeFiles/bam-load.dir/reference-writer.c.o.d -o CMakeFiles/bam-load.dir/reference-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/reference-writer.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/cg-load.c: In function 'DB_Fini': /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/cg-load.c:229:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 229 | if( (rc = KLoaderMeta_Write(node, p->argv0, __DATE__, "Complete Genomics", KAppVersion())) != 0 ) { | ^~~~~~~~ -[ 51%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/run-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/run-xml.c.o -MF CMakeFiles/abi-load.dir/run-xml.c.o.d -o CMakeFiles/abi-load.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c -[ 51%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o -MF CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o.d -o CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/hdf5/hdf5file.c -[ 51%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/reference-writer.c.o -[ 52%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/config.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT 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/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sorting-row-set.c.o -MF CMakeFiles/sra-sort.dir/sorting-row-set.c.o.d -o CMakeFiles/sra-sort.dir/sorting-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sorting-row-set.c +[ 54%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/meta-pair.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/meta-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/meta-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/meta-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/meta-pair.c +[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/sra-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/sra-writer.c.o -MF CMakeFiles/abi-load.dir/sra-writer.c.o.d -o CMakeFiles/abi-load.dir/sra-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c +[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-file.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-file.c.o -MF CMakeFiles/srf-load.dir/loader-file.c.o.d -o CMakeFiles/srf-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ -[ 52%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-file.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-file.c.o -MF CMakeFiles/srf-load.dir/loader-file.c.o.d -o CMakeFiles/srf-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c -[ 53%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-context.c.o +[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/sra-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/sra-writer.c.o -MF CMakeFiles/fastq-load.dir/sra-writer.c.o.d -o CMakeFiles/fastq-load.dir/sra-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c +[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-file.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-file.c.o -MF CMakeFiles/sff-load.dir/loader-file.c.o.d -o CMakeFiles/sff-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c +/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/config.cpp:101:13: warning: 'bool sratools::forceInstallID()' defined but not used [-Wunused-function] + 101 | static bool forceInstallID(void) + | ^~~~~~~~~~~~~~ +[ 54%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o -MF CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o.d -o CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/hdf5/hdf5file.c +[ 55%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-fmt.c.o +[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/writer-helicos.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-fmt.c.o -MF CMakeFiles/sff-load.dir/loader-fmt.c.o.d -o 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-D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/command-line.cpp.o -MF CMakeFiles/sratools.dir/command-line.cpp.o.d -o CMakeFiles/sratools.dir/command-line.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/command-line.cpp +[ 56%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-context.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-context.c.o -MF CMakeFiles/pacbio-load.dir/pl-context.c.o.d -o CMakeFiles/pacbio-load.dir/pl-context.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-context.c -[ 53%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb_info.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb_info.c.o -MF CMakeFiles/vdb-dump.dir/vdb_info.c.o.d -o CMakeFiles/vdb-dump.dir/vdb_info.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c -[ 53%] Linking C static library ../../../ilib/libfastqloader.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -P CMakeFiles/fastqloader.dir/cmake_clean_target.cmake -[ 53%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sequence-writer.c.o +[ 56%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sequence-writer.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sequence-writer.c.o -MF CMakeFiles/bam-load.dir/sequence-writer.c.o.d -o CMakeFiles/bam-load.dir/sequence-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sequence-writer.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastqloader.dir/link.txt --verbose=1 -/usr/bin/ar qc ../../../ilib/libfastqloader.a "CMakeFiles/fastqloader.dir/spot-assembler.c.o" "CMakeFiles/fastqloader.dir/common-writer.c.o" "CMakeFiles/fastqloader.dir/sequence-writer.c.o" "CMakeFiles/fastqloader.dir/common-reader.c.o" "CMakeFiles/fastqloader.dir/fastq-reader.c.o" "CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o" "CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o" CMakeFiles/fastqloader.dir/id2name.c.o -/usr/bin/ranlib ../../../ilib/libfastqloader.a -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 53%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/sra-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/sra-writer.c.o -MF CMakeFiles/fastq-load.dir/sra-writer.c.o.d -o CMakeFiles/fastq-load.dir/sra-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c -[ 54%] Built target fastqloader -make -f tools/loaders/general-loader/CMakeFiles/general-loader.dir/build.make tools/loaders/general-loader/CMakeFiles/general-loader.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/CMakeFiles/general-loader.dir/DependInfo.cmake --color= +[ 56%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/dir-pair.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/dir-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/dir-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/dir-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/dir-pair.c +[ 56%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat 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tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader.c.o -MF CMakeFiles/abi-load.dir/loader.c.o.d -o CMakeFiles/abi-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c +[ 57%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader.c.o -MF CMakeFiles/fastq-load.dir/loader.c.o.d -o CMakeFiles/fastq-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sequence-writer.c: In function 'SequenceWhack': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sequence-writer.c:490:14: warning: unused variable 'rc' [-Wunused-variable] 490 | rc_t rc = VDatabaseOpenTableUpdate(self->db, &tbl, "SEQUENCE"); | ^~ -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/general-loader/CMakeFiles/general-loader.dir/build.make tools/loaders/general-loader/CMakeFiles/general-loader.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 54%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-tools.c.o +[ 57%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/helicos-fmt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/helicos-fmt.c.o -MF CMakeFiles/helicos-load.dir/helicos-fmt.c.o.d -o CMakeFiles/helicos-load.dir/helicos-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/helicos-fmt.c +[ 57%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/sra-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/sra-writer.c.o -MF CMakeFiles/sff-load.dir/sra-writer.c.o.d -o CMakeFiles/sff-load.dir/sra-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c +[ 57%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-tools.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-tools.c.o -MF CMakeFiles/pacbio-load.dir/pl-tools.c.o.d -o CMakeFiles/pacbio-load.dir/pl-tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-tools.c -[ 54%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/general-loader.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/general-loader.cpp.o -MF CMakeFiles/general-loader.dir/general-loader.cpp.o.d -o CMakeFiles/general-loader.dir/general-loader.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/general-loader.cpp -[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-fmt.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-fmt.c.o -MF CMakeFiles/srf-load.dir/loader-fmt.c.o.d -o CMakeFiles/srf-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c -[ 54%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] + 711 | const char* b = NULL; + | ^ +[ 57%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/dir-pair.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/dir-pair.c.o -MF CMakeFiles/sra-sort.dir/dir-pair.c.o.d -o CMakeFiles/sra-sort.dir/dir-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/dir-pair.c +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); + | ^~~~~~~~ +[ 57%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-fmt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-fmt.c.o -MF CMakeFiles/illumina-load.dir/loader-fmt.c.o.d -o CMakeFiles/illumina-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); + | ^~~~~~~~ +[ 57%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/tbl-pair.c -[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/run-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/run-xml.c.o -MF CMakeFiles/helicos-load.dir/run-xml.c.o.d -o CMakeFiles/helicos-load.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c -[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/sra-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/sra-writer.c.o -MF CMakeFiles/srf-load.dir/sra-writer.c.o.d -o CMakeFiles/srf-load.dir/sra-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c -[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-file.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-file.c.o -MF CMakeFiles/abi-load.dir/loader-file.c.o.d -o CMakeFiles/abi-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c -[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/run-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/run-xml.c.o -MF CMakeFiles/pacbio-loadxml.dir/run-xml.c.o.d -o CMakeFiles/pacbio-loadxml.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c -[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/run-xml.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/run-xml.c.o -MF CMakeFiles/illumina-load.dir/run-xml.c.o.d -o CMakeFiles/illumina-load.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c -[ 54%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/db-pair.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/db-pair.c.o -MF CMakeFiles/sra-sort.dir/db-pair.c.o.d -o CMakeFiles/sra-sort.dir/db-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/db-pair.c -[ 54%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/loader-imp.c.o +[ 57%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/sra-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/sra-writer.c.o -MF CMakeFiles/illumina-load.dir/sra-writer.c.o.d -o CMakeFiles/illumina-load.dir/sra-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c +[ 57%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader.c.o +[ 57%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/writer-absolid.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader.c.o -MF CMakeFiles/sff-load.dir/loader.c.o.d -o CMakeFiles/sff-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/writer-absolid.c.o -MF CMakeFiles/abi-load.dir/writer-absolid.c.o.d -o CMakeFiles/abi-load.dir/writer-absolid.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-absolid.c +[ 57%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/loader-imp.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/loader-imp.c.o -MF CMakeFiles/bam-load.dir/loader-imp.c.o.d -o CMakeFiles/bam-load.dir/loader-imp.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c -In function 'inspect_line', - inlined from 'parse_buffer' at /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:602:29, - inlined from 'get_meta_bam_hdr' at /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:639:21, - inlined from 'get_meta_info' at /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:681:5: -/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:575:43: warning: 'line' may be used uninitialized [-Wmaybe-uninitialized] - 575 | case 'P' : if ( 'G' == line[ 2 ] ) ( bam_hdr -> PG_lines )++; break; - | ~~~~^~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c: In function 'get_meta_info': -/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:582:12: note: 'line' was declared here - 582 | char * line; - | ^~~~ -[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader.c.o -MF CMakeFiles/fastq-load.dir/loader.c.o.d -o CMakeFiles/fastq-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c -[ 54%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o -MF CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o.d -o CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-evidence-intervals.c -[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-fmt.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-fmt.c.o -MF CMakeFiles/abi-load.dir/loader-fmt.c.o.d -o CMakeFiles/abi-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c -[ 54%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-zmw.c.o +[ 57%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader.c.o -MF CMakeFiles/srf-load.dir/loader.c.o.d -o CMakeFiles/srf-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); + | ^~~~~~~~ +[ 57%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-zmw.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-zmw.c.o -MF CMakeFiles/pacbio-load.dir/pl-zmw.c.o.d -o CMakeFiles/pacbio-load.dir/pl-zmw.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-zmw.c -[ 54%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader.c.o +[ 57%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o -MF CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o.d -o CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-evidence-intervals.c +[ 57%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/tbl-pair.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/tbl-pair.c.o -MF CMakeFiles/sra-sort.dir/tbl-pair.c.o.d -o CMakeFiles/sra-sort.dir/tbl-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/tbl-pair.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader.c.o -MF CMakeFiles/srf-load.dir/loader.c.o.d -o CMakeFiles/srf-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ -[ 55%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/db-pair.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/db-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/db-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/db-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/db-pair.c -[ 55%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-454.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-454.c.o -MF CMakeFiles/sff-load.dir/writer-454.c.o.d -o CMakeFiles/sff-load.dir/writer-454.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-454.c +[ 57%] Linking C executable ../../../bin/helicos-load +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/helicos-load.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/helicos-load.dir/pstring.c.o" "CMakeFiles/helicos-load.dir/common-xml.c.o" "CMakeFiles/helicos-load.dir/experiment-xml.c.o" "CMakeFiles/helicos-load.dir/run-xml.c.o" "CMakeFiles/helicos-load.dir/loader-file.c.o" "CMakeFiles/helicos-load.dir/loader-fmt.c.o" "CMakeFiles/helicos-load.dir/sra-writer.c.o" "CMakeFiles/helicos-load.dir/loader.c.o" "CMakeFiles/helicos-load.dir/writer-helicos.c.o" "CMakeFiles/helicos-load.dir/helicos-fmt.c.o" -o ../../../bin/helicos-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so +[ 57%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader.c.o -MF CMakeFiles/illumina-load.dir/loader.c.o.d -o CMakeFiles/illumina-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f helicos-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv helicos-load helicos-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s helicos-load.3.0.3 helicos-load.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s helicos-load.3 helicos-load /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ -[ 55%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/sra-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/sra-writer.c.o -MF CMakeFiles/abi-load.dir/sra-writer.c.o.d -o CMakeFiles/abi-load.dir/sra-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c -[ 55%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 57%] Built target helicos-load +make -f tools/loaders/general-loader/CMakeFiles/general-loader.dir/build.make tools/loaders/general-loader/CMakeFiles/general-loader.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/CMakeFiles/general-loader.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/loaders/general-loader/CMakeFiles/general-loader.dir/build.make tools/loaders/general-loader/CMakeFiles/general-loader.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 57%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o -MF CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o.d -o CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-basecalls_cmn.c -[ 55%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-sequence.c.o -[ 55%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/glob-poslen.c.o +[ 57%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/general-loader.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/general-loader.cpp.o -MF CMakeFiles/general-loader.dir/general-loader.cpp.o.d -o CMakeFiles/general-loader.dir/general-loader.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/general-loader.cpp +[ 57%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/absolid-fmt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/absolid-fmt.c.o -MF CMakeFiles/abi-load.dir/absolid-fmt.c.o.d -o CMakeFiles/abi-load.dir/absolid-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/absolid-fmt.c +[ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/db-pair.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/db-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/db-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/db-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/db-pair.c +[ 58%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-sequence.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-sequence.c.o -MF CMakeFiles/pacbio-load.dir/pl-sequence.c.o.d -o CMakeFiles/pacbio-load.dir/pl-sequence.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-sequence.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/glob-poslen.c.o -MF CMakeFiles/sra-sort.dir/glob-poslen.c.o.d -o CMakeFiles/sra-sort.dir/glob-poslen.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/glob-poslen.c -/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/config.cpp:101:13: warning: 'bool sratools::forceInstallID()' defined but not used [-Wunused-function] - 101 | static bool forceInstallID(void) - | ^~~~~~~~~~~~~~ -[ 55%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-file.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-file.c.o -MF CMakeFiles/pacbio-loadxml.dir/loader-file.c.o.d -o CMakeFiles/pacbio-loadxml.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c -[ 56%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-file.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-file.c.o -MF CMakeFiles/helicos-load.dir/loader-file.c.o.d -o CMakeFiles/helicos-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c -[ 56%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-ion-torrent.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-ion-torrent.c.o -MF CMakeFiles/sff-load.dir/writer-ion-torrent.c.o.d -o CMakeFiles/sff-load.dir/writer-ion-torrent.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-ion-torrent.c -[ 56%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-fmt.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-fmt.c.o -MF CMakeFiles/helicos-load.dir/loader-fmt.c.o.d -o CMakeFiles/helicos-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c -[ 56%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump.c -[ 57%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader.c.o -[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o -MF CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o.d -o CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader.c.o -MF CMakeFiles/abi-load.dir/loader.c.o.d -o CMakeFiles/abi-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c -[ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/poslen-col-pair.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/poslen-col-pair.c.o -MF CMakeFiles/sra-sort.dir/poslen-col-pair.c.o.d -o CMakeFiles/sra-sort.dir/poslen-col-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/poslen-col-pair.c -[ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o -MF CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o.d -o CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/glob-poslen.c -[ 58%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/protocol-parser.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/protocol-parser.cpp.o -MF CMakeFiles/general-loader.dir/protocol-parser.cpp.o.d -o CMakeFiles/general-loader.dir/protocol-parser.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/protocol-parser.cpp -[ 58%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o -MF CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o.d -o CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-evidence-dnbs.c -[ 58%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/command-line.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/command-line.cpp.o -MF CMakeFiles/sratools.dir/command-line.cpp.o.d -o CMakeFiles/sratools.dir/command-line.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/command-line.cpp +[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/run-xml.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/run-xml.c.o -MF CMakeFiles/pacbio-loadxml.dir/run-xml.c.o.d -o CMakeFiles/pacbio-loadxml.dir/run-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:4172:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 4172 | rc = KLoaderMeta_Write(node, progName, __DATE__, "BAM", KAppVersion()); | ^~~~~~~~ -[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-file.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-file.c.o -MF CMakeFiles/illumina-load.dir/loader-file.c.o.d -o CMakeFiles/illumina-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c -[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/sra-writer.c.o -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); - | ^~~~~~~~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/sra-writer.c.o -MF CMakeFiles/helicos-load.dir/sra-writer.c.o.d -o CMakeFiles/helicos-load.dir/sra-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-illumina.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-illumina.c.o -MF CMakeFiles/fastq-load.dir/writer-illumina.c.o.d -o CMakeFiles/fastq-load.dir/writer-illumina.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-illumina.c +[ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/db-pair.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/db-pair.c.o -MF CMakeFiles/sra-sort.dir/db-pair.c.o.d -o CMakeFiles/sra-sort.dir/db-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/db-pair.c +[ 58%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o -MF CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o.d -o CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-evidence-dnbs.c +[ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/glob-poslen.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/glob-poslen.c.o -MF CMakeFiles/sra-sort.dir/glob-poslen.c.o.d -o CMakeFiles/sra-sort.dir/glob-poslen.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/glob-poslen.c +[ 58%] Linking C executable ../../../bin/abi-load +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/abi-load.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/abi-load.dir/pstring.c.o" "CMakeFiles/abi-load.dir/common-xml.c.o" "CMakeFiles/abi-load.dir/experiment-xml.c.o" "CMakeFiles/abi-load.dir/run-xml.c.o" "CMakeFiles/abi-load.dir/loader-file.c.o" "CMakeFiles/abi-load.dir/loader-fmt.c.o" "CMakeFiles/abi-load.dir/sra-writer.c.o" "CMakeFiles/abi-load.dir/loader.c.o" "CMakeFiles/abi-load.dir/writer-absolid.c.o" "CMakeFiles/abi-load.dir/absolid-fmt.c.o" -o ../../../bin/abi-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f abi-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv abi-load abi-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-load.3.0.3 abi-load.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-load.3 abi-load +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-454.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-454.c.o -MF CMakeFiles/sff-load.dir/writer-454.c.o.d -o CMakeFiles/sff-load.dir/writer-454.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-454.c +[ 58%] Built target abi-load +make -f tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/poslen-col-pair.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/poslen-col-pair.c.o -MF CMakeFiles/sra-sort.dir/poslen-col-pair.c.o.d -o CMakeFiles/sra-sort.dir/poslen-col-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/poslen-col-pair.c +[ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o -MF CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o.d -o CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/glob-poslen.c +[ 58%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o -MF CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o.d -o CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp [ 58%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-consensus.c.o -[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o -MF CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o.d -o CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-consensus.c.o -MF CMakeFiles/pacbio-load.dir/pl-consensus.c.o.d -o CMakeFiles/pacbio-load.dir/pl-consensus.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-consensus.c -[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/sff-fmt.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/sff-fmt.c.o -MF CMakeFiles/sff-load.dir/sff-fmt.c.o.d -o CMakeFiles/sff-load.dir/sff-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sff-fmt.c +[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/writer-illumina.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/writer-illumina.c.o -MF CMakeFiles/illumina-load.dir/writer-illumina.c.o.d -o CMakeFiles/illumina-load.dir/writer-illumina.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-illumina.c +[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf.c.o -MF CMakeFiles/srf-load.dir/srf.c.o.d -o CMakeFiles/srf-load.dir/srf.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf.c +[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-454.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-454.c.o -MF CMakeFiles/fastq-load.dir/writer-454.c.o.d -o CMakeFiles/fastq-load.dir/writer-454.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-454.c +[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-file.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-file.c.o -MF CMakeFiles/pacbio-loadxml.dir/loader-file.c.o.d -o CMakeFiles/pacbio-loadxml.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c +In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp:32: +/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/../database-loader.cpp:699:90: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 699 | rc = KLoaderMeta_WriteWithVersion ( node, m_programName.c_str(), __DATE__, KAppVersion(), m_softwareName.c_str(), m_softwareVersion ); + | ^~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp:619:86: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 619 | REQUIRE_EQ ( string ( __DATE__), GetDbMetadataAttr ( "SOFTWARE/loader", "date" ) ); + | ^ [ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/poslen-col-pair.c -[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-fmt.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-fmt.c.o -MF CMakeFiles/illumina-load.dir/loader-fmt.c.o.d -o CMakeFiles/illumina-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c +[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-fmt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-fmt.c.o -MF CMakeFiles/srf-load.dir/srf-fmt.c.o.d -o CMakeFiles/srf-load.dir/srf-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-fmt.c [ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/ref-alignid-col.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/ref-alignid-col.c.o -MF CMakeFiles/sra-sort.dir/ref-alignid-col.c.o.d -o CMakeFiles/sra-sort.dir/ref-alignid-col.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ref-alignid-col.c -[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader.c.o -MF CMakeFiles/helicos-load.dir/loader.c.o.d -o CMakeFiles/helicos-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c -[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/buff-writer.c.o -MF CMakeFiles/sra-sort.dir/buff-writer.c.o.d -o CMakeFiles/sra-sort.dir/buff-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/buff-writer.c +[ 60%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-passes.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-passes.c.o -MF CMakeFiles/pacbio-load.dir/pl-passes.c.o.d -o CMakeFiles/pacbio-load.dir/pl-passes.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-passes.c -[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/sra-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux 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-I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-fmt.c.o -MF CMakeFiles/srf-load.dir/srf-fmt.c.o.d -o CMakeFiles/srf-load.dir/srf-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-fmt.c -[ 58%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader.c.o -MF CMakeFiles/pacbio-loadxml.dir/loader.c.o.d -o CMakeFiles/pacbio-loadxml.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c -[ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o +[ 60%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-ion-torrent.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-ion-torrent.c.o -MF CMakeFiles/sff-load.dir/writer-ion-torrent.c.o.d -o CMakeFiles/sff-load.dir/writer-ion-torrent.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-ion-torrent.c +[ 60%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/protocol-parser.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/protocol-parser.cpp.o -MF CMakeFiles/general-loader.dir/protocol-parser.cpp.o.d -o CMakeFiles/general-loader.dir/protocol-parser.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/protocol-parser.cpp +[ 61%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/illumina-fmt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/illumina-fmt.c.o -MF CMakeFiles/illumina-load.dir/illumina-fmt.c.o.d -o CMakeFiles/illumina-load.dir/illumina-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/illumina-fmt.c +[ 61%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/run-source.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/run-source.cpp.o -MF CMakeFiles/sratools.dir/run-source.cpp.o.d -o CMakeFiles/sratools.dir/run-source.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/run-source.cpp +[ 61%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o -MF CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o.d -o CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c +[ 61%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o -MF CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o.d -o CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ref-alignid-col.c -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); - | ^~~~~~~~ -[ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/buff-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/buff-writer.c.o -MF CMakeFiles/sra-sort.dir/buff-writer.c.o.d -o CMakeFiles/sra-sort.dir/buff-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/buff-writer.c -[ 59%] Linking C executable ../../../bin/sff-load -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/sff-load.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sff-load.dir/pstring.c.o" "CMakeFiles/sff-load.dir/common-xml.c.o" "CMakeFiles/sff-load.dir/experiment-xml.c.o" "CMakeFiles/sff-load.dir/run-xml.c.o" "CMakeFiles/sff-load.dir/loader-file.c.o" "CMakeFiles/sff-load.dir/loader-fmt.c.o" "CMakeFiles/sff-load.dir/sra-writer.c.o" "CMakeFiles/sff-load.dir/loader.c.o" "CMakeFiles/sff-load.dir/writer-454.c.o" "CMakeFiles/sff-load.dir/writer-ion-torrent.c.o" "CMakeFiles/sff-load.dir/sff-fmt.c.o" -o ../../../bin/sff-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so -[ 59%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader.c.o -MF CMakeFiles/illumina-load.dir/loader.c.o.d -o CMakeFiles/illumina-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c -[ 59%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-illumina.c.o +[ 61%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o -MF CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o.d -o CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-ion-torrent.c +[ 61%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-illumina.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-illumina.c.o -MF CMakeFiles/srf-load.dir/writer-illumina.c.o.d -o CMakeFiles/srf-load.dir/writer-illumina.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-illumina.c -[ 59%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-metrics.c.o +[ 61%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/id-mapper-col.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/id-mapper-col.c.o -MF CMakeFiles/sra-sort.dir/id-mapper-col.c.o.d -o CMakeFiles/sra-sort.dir/id-mapper-col.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/id-mapper-col.c +[ 61%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-metrics.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-metrics.c.o -MF CMakeFiles/pacbio-load.dir/pl-metrics.c.o.d -o CMakeFiles/pacbio-load.dir/pl-metrics.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-metrics.c +[ 61%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-mappings.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-mappings.c.o -MF CMakeFiles/cg-load.dir/factory-mappings.c.o.d -o CMakeFiles/cg-load.dir/factory-mappings.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c +[ 61%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/sff-fmt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/sff-fmt.c.o -MF CMakeFiles/sff-load.dir/sff-fmt.c.o.d -o CMakeFiles/sff-load.dir/sff-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sff-fmt.c +[ 61%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader.c.o -MF CMakeFiles/pacbio-loadxml.dir/loader.c.o.d -o CMakeFiles/pacbio-loadxml.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c +[ 61%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o -MF CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o.d -o CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/capture-first-half-aligned.c +[ 61%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/run.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/run.c.o -MF CMakeFiles/sra-sort.dir/run.c.o.d -o CMakeFiles/sra-sort.dir/run.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/run.c +[ 61%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/fastq-fmt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/fastq-fmt.c.o -MF CMakeFiles/fastq-load.dir/fastq-fmt.c.o.d -o CMakeFiles/fastq-load.dir/fastq-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/fastq-fmt.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ -[ 59%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/writer-absolid.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/writer-absolid.c.o -MF CMakeFiles/abi-load.dir/writer-absolid.c.o.d -o CMakeFiles/abi-load.dir/writer-absolid.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-absolid.c -[ 59%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-454.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sff-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-454.c.o -MF CMakeFiles/fastq-load.dir/writer-454.c.o.d -o CMakeFiles/fastq-load.dir/writer-454.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-454.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sff-load sff-load.3.0.3 -[ 59%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-mappings.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-load.3.0.3 sff-load.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-mappings.c.o -MF CMakeFiles/cg-load.dir/factory-mappings.c.o.d -o CMakeFiles/cg-load.dir/factory-mappings.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-load.3 sff-load -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 59%] Built target sff-load -[ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/id-mapper-col.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/id-mapper-col.c.o -MF CMakeFiles/sra-sort.dir/id-mapper-col.c.o.d -o CMakeFiles/sra-sort.dir/id-mapper-col.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/id-mapper-col.c -[ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/buff-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/buff-writer.c.o -MF CMakeFiles/sra-sort-cg.dir/buff-writer.c.o.d -o CMakeFiles/sra-sort-cg.dir/buff-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/buff-writer.c +[ 61%] Linking C executable ../../../bin/illumina-load +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/illumina-load.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/illumina-load.dir/pstring.c.o" "CMakeFiles/illumina-load.dir/common-xml.c.o" "CMakeFiles/illumina-load.dir/experiment-xml.c.o" "CMakeFiles/illumina-load.dir/run-xml.c.o" "CMakeFiles/illumina-load.dir/loader-file.c.o" "CMakeFiles/illumina-load.dir/loader-fmt.c.o" "CMakeFiles/illumina-load.dir/sra-writer.c.o" "CMakeFiles/illumina-load.dir/loader.c.o" "CMakeFiles/illumina-load.dir/writer-illumina.c.o" "CMakeFiles/illumina-load.dir/illumina-fmt.c.o" -o ../../../bin/illumina-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings15_Read': /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:248:16: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] 248 | if( tmp[0] < 33 || tmp[0] > 126 ) { @@ -4986,14 +5077,13 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:225:14: note: 'tmp' declared here 225 | char tmp[2]; | ^~~ -[ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char 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tools/loaders/sra-load/CMakeFiles/abi-load.dir/absolid-fmt.c.o -MF CMakeFiles/abi-load.dir/absolid-fmt.c.o.d -o CMakeFiles/abi-load.dir/absolid-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/absolid-fmt.c -[ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/run.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/run.c.o -MF CMakeFiles/sra-sort.dir/run.c.o.d -o CMakeFiles/sra-sort.dir/run.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/run.c +[ 61%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/buff-writer.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/buff-writer.c.o -MF CMakeFiles/sra-sort-cg.dir/buff-writer.c.o.d -o CMakeFiles/sra-sort-cg.dir/buff-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/buff-writer.c +[ 61%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sra-sort.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sra-sort.c.o -MF CMakeFiles/sra-sort.dir/sra-sort.c.o.d -o CMakeFiles/sra-sort.dir/sra-sort.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sra-sort.c +[ 62%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-illumina.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-illumina.c.o -MF CMakeFiles/srf-load.dir/ztr-illumina.c.o.d -o CMakeFiles/srf-load.dir/ztr-illumina.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/ztr-illumina.c +[ 62%] Linking C executable ../../../bin/sff-load /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings22_Read': /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:311:16: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] 311 | if( tmp[0] < 33 || tmp[0] > 126 ) { @@ -5001,151 +5091,56 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:287:14: note: 'tmp' declared here 287 | char tmp[2]; | ^~~ -[ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sra-sort.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sra-sort.c.o -MF CMakeFiles/sra-sort.dir/sra-sort.c.o.d -o CMakeFiles/sra-sort.dir/sra-sort.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sra-sort.c -[ 59%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/writer-helicos.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time 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-rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o -MF CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o.d -o CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/id-mapper-col.c -[ 60%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-illumina.c.o -/build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings25_Read': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:382:16: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] - 382 | if( tmp[0] < 33 || tmp[0] > 126 ) { - | ~~~^~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:358:14: note: 'tmp' declared here - 358 | char tmp[2]; - | ^~~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb 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/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-regions.c.o -MF CMakeFiles/pacbio-load.dir/pl-regions.c.o.d -o CMakeFiles/pacbio-load.dir/pl-regions.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-regions.c -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o" "CMakeFiles/vdb-dump.dir/vdb_info.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump.c.o" -o ../../../bin/vdb-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 62%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 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-I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-reads.c.o -MF CMakeFiles/cg-load.dir/factory-reads.c.o.d -o CMakeFiles/cg-load.dir/factory-reads.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-reads.c -[ 63%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o -MF CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o.d -o CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/capture-first-half-aligned.c -[ 63%] Linking C executable ../../../bin/pacbio-loadxml -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/pacbio-loadxml.dir/link.txt --verbose=1 -[ 63%] Linking C executable ../../../bin/abi-load -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/abi-load.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-dump.3.0.3 -[ 63%] Linking C executable ../../../bin/helicos-load -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/helicos-load.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/pacbio-loadxml.dir/pstring.c.o" "CMakeFiles/pacbio-loadxml.dir/common-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/run-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/loader-file.c.o" "CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o" "CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o" "CMakeFiles/pacbio-loadxml.dir/loader.c.o" "CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o" -o ../../../bin/pacbio-loadxml ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-dump vdb-dump.3.0.3 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/abi-load.dir/pstring.c.o" "CMakeFiles/abi-load.dir/common-xml.c.o" "CMakeFiles/abi-load.dir/experiment-xml.c.o" "CMakeFiles/abi-load.dir/run-xml.c.o" "CMakeFiles/abi-load.dir/loader-file.c.o" "CMakeFiles/abi-load.dir/loader-fmt.c.o" "CMakeFiles/abi-load.dir/sra-writer.c.o" "CMakeFiles/abi-load.dir/loader.c.o" "CMakeFiles/abi-load.dir/writer-absolid.c.o" "CMakeFiles/abi-load.dir/absolid-fmt.c.o" -o ../../../bin/abi-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-dump.3.0.3 vdb-dump.3 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/helicos-load.dir/pstring.c.o" "CMakeFiles/helicos-load.dir/common-xml.c.o" "CMakeFiles/helicos-load.dir/experiment-xml.c.o" "CMakeFiles/helicos-load.dir/run-xml.c.o" "CMakeFiles/helicos-load.dir/loader-file.c.o" "CMakeFiles/helicos-load.dir/loader-fmt.c.o" "CMakeFiles/helicos-load.dir/sra-writer.c.o" "CMakeFiles/helicos-load.dir/loader.c.o" "CMakeFiles/helicos-load.dir/writer-helicos.c.o" "CMakeFiles/helicos-load.dir/helicos-fmt.c.o" -o ../../../bin/helicos-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-dump.3 vdb-dump -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 vdb-dump-driver -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 63%] Built target vdb-dump -make -f tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/DependInfo.cmake --color= +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sff-load.dir/pstring.c.o" "CMakeFiles/sff-load.dir/common-xml.c.o" "CMakeFiles/sff-load.dir/experiment-xml.c.o" "CMakeFiles/sff-load.dir/run-xml.c.o" "CMakeFiles/sff-load.dir/loader-file.c.o" "CMakeFiles/sff-load.dir/loader-fmt.c.o" "CMakeFiles/sff-load.dir/sra-writer.c.o" "CMakeFiles/sff-load.dir/loader.c.o" "CMakeFiles/sff-load.dir/writer-454.c.o" "CMakeFiles/sff-load.dir/writer-ion-torrent.c.o" "CMakeFiles/sff-load.dir/sff-fmt.c.o" -o ../../../bin/sff-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f illumina-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv illumina-load illumina-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-load.3.0.3 illumina-load.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-load.3 illumina-load make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 62%] Built target illumina-load make -f tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/depend -[ 63%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o -MF CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o.d -o CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp -[ 63%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/run.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/run.c.o -MF CMakeFiles/sra-sort-cg.dir/run.c.o.d -o CMakeFiles/sra-sort-cg.dir/run.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/run.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 63%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o +[ 62%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o -MF CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o.d -o CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-gw-dumper.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f helicos-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv helicos-load helicos-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s helicos-load.3.0.3 helicos-load.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s helicos-load.3 helicos-load -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f abi-load.3.0.3 -[ 63%] Linking C executable ../../../bin/sra-sort -[ 63%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-progress.c.o +[ 62%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-tbl.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-tbl.c.o -MF CMakeFiles/sra-sort.dir/csra-tbl.c.o.d -o CMakeFiles/sra-sort.dir/csra-tbl.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-tbl.c +/build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings25_Read': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:382:16: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] + 382 | if( tmp[0] < 33 || tmp[0] > 126 ) { + | ~~~^~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:358:14: note: 'tmp' declared here + 358 | char tmp[2]; + | ^~~ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sff-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sff-load sff-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-load.3.0.3 sff-load.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-load.3 sff-load make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-sort.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-progress.c.o -MF CMakeFiles/pacbio-load.dir/pl-progress.c.o.d -o CMakeFiles/pacbio-load.dir/pl-progress.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-progress.c -In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp:32: -/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/../database-loader.cpp:699:90: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 699 | rc = KLoaderMeta_WriteWithVersion ( node, m_programName.c_str(), __DATE__, KAppVersion(), m_softwareName.c_str(), m_softwareVersion ); - | ^~~~~~~~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv abi-load abi-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-load.3.0.3 abi-load.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-loadxml.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-loadxml pacbio-loadxml.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-load.3 abi-load -[ 63%] Built target helicos-load +[ 62%] Built target sff-load make -f tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/build.make tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/depend -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-loadxml.3.0.3 pacbio-loadxml.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/DependInfo.cmake --color= -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-sort.dir/caps.c.o" "CMakeFiles/sra-sort.dir/mem.c.o" "CMakeFiles/sra-sort.dir/membank.c.o" "CMakeFiles/sra-sort.dir/paged-membank.c.o" "CMakeFiles/sra-sort.dir/paged-mmapbank.c.o" "CMakeFiles/sra-sort.dir/except.c.o" "CMakeFiles/sra-sort.dir/idx-mapping.c.o" "CMakeFiles/sra-sort.dir/map-file.c.o" "CMakeFiles/sra-sort.dir/col-pair.c.o" "CMakeFiles/sra-sort.dir/row-set.c.o" "CMakeFiles/sra-sort.dir/simple-row-set.c.o" "CMakeFiles/sra-sort.dir/mapping-row-set.c.o" "CMakeFiles/sra-sort.dir/sorting-row-set.c.o" "CMakeFiles/sra-sort.dir/meta-pair.c.o" "CMakeFiles/sra-sort.dir/dir-pair.c.o" "CMakeFiles/sra-sort.dir/tbl-pair.c.o" "CMakeFiles/sra-sort.dir/db-pair.c.o" "CMakeFiles/sra-sort.dir/glob-poslen.c.o" "CMakeFiles/sra-sort.dir/poslen-col-pair.c.o" "CMakeFiles/sra-sort.dir/ref-alignid-col.c.o" "CMakeFiles/sra-sort.dir/buff-writer.c.o" "CMakeFiles/sra-sort.dir/id-mapper-col.c.o" "CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o" "CMakeFiles/sra-sort.dir/run.c.o" "CMakeFiles/sra-sort.dir/sra-sort.c.o" "CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o" "CMakeFiles/sra-sort.dir/csra-tbl.c.o" "CMakeFiles/sra-sort.dir/csra-pair.c.o" -o ../../../bin/sra-sort /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -lbz2 -llzma -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-loadxml.3 pacbio-loadxml -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 63%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/writer-illumina.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/writer-illumina.c.o -MF CMakeFiles/illumina-load.dir/writer-illumina.c.o.d -o CMakeFiles/illumina-load.dir/writer-illumina.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-illumina.c -/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp:619:86: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 619 | REQUIRE_EQ ( string ( __DATE__), GetDbMetadataAttr ( "SOFTWARE/loader", "date" ) ); - | ^ +[ 62%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-pair.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-pair.c.o -MF CMakeFiles/sra-sort.dir/csra-pair.c.o.d -o CMakeFiles/sra-sort.dir/csra-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-pair.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/build.make tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 63%] Built target abi-load -make -f tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/DependInfo.cmake --color= -[ 63%] Built target pacbio-loadxml -make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/depend -[ 63%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/run-source.cpp.o -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema 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CMakeFiles/makeinputs.dir/makeinputs.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/makeinputs.cpp -[ 63%] Linking C executable ../../../bin/fastq-load +[ 62%] Linking C executable ../../../bin/fastq-load cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastq-load.dir/link.txt --verbose=1 -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 63%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-tag-lfr.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 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Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/fastq-load.dir/pstring.c.o" "CMakeFiles/fastq-load.dir/common-xml.c.o" "CMakeFiles/fastq-load.dir/experiment-xml.c.o" "CMakeFiles/fastq-load.dir/run-xml.c.o" "CMakeFiles/fastq-load.dir/loader-file.c.o" "CMakeFiles/fastq-load.dir/loader-fmt.c.o" "CMakeFiles/fastq-load.dir/sra-writer.c.o" "CMakeFiles/fastq-load.dir/loader.c.o" "CMakeFiles/fastq-load.dir/writer-illumina.c.o" "CMakeFiles/fastq-load.dir/writer-454.c.o" "CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o" "CMakeFiles/fastq-load.dir/fastq-fmt.c.o" -o ../../../bin/fastq-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o -MF CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o.d -o CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp -[ 63%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sra-sort.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sra-sort.c.o -MF CMakeFiles/sra-sort-cg.dir/sra-sort.c.o.d -o CMakeFiles/sra-sort-cg.dir/sra-sort.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sra-sort.c -[ 63%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o -MF CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o.d -o CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp -[ 63%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-illumina.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-illumina.c.o -MF CMakeFiles/srf-load.dir/srf-illumina.c.o.d -o CMakeFiles/srf-load.dir/srf-illumina.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-illumina.c -[ 63%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pacbio-load.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pacbio-load.c.o -MF CMakeFiles/pacbio-load.dir/pacbio-load.c.o.d -o CMakeFiles/pacbio-load.dir/pacbio-load.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pacbio-load.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-sort.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-sort sra-sort.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort.3.0.3 sra-sort.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort.3 sra-sort -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pacbio-load.c: In function 'pacbio_meta_entry': +[ 63%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-reads.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-reads.c.o -MF CMakeFiles/cg-load.dir/factory-reads.c.o.d -o CMakeFiles/cg-load.dir/factory-reads.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-reads.c +[ 64%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-regions.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-regions.c.o -MF CMakeFiles/pacbio-load.dir/pl-regions.c.o.d -o CMakeFiles/pacbio-load.dir/pl-regions.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-regions.c In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/logger-inl.h:12, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/logger.h:446, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/details/registry-inl.h:12, @@ -5163,10 +5158,8 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter-inl.h:1017:15: warning: when initialized here [-Wreorder] 1017 | SPDLOG_INLINE pattern_formatter::pattern_formatter( | ^~~~~~~~~~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pacbio-load.c:219:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 219 | rc = KLoaderMeta_Write( node, toolname, __DATE__, "PacBio HDF5", KAppVersion() ); - | ^~~~~~~~ -[ 63%] Built target sra-sort +[ 64%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o -MF CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o.d -o CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/id-mapper-col.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h: In constructor 'spdlog::pattern_formatter::pattern_formatter(spdlog::pattern_time_type, std::string)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:108:26: warning: 'spdlog::pattern_formatter::last_log_secs_' will be initialized after [-Wreorder] 108 | std::chrono::seconds last_log_secs_; @@ -5174,261 +5167,312 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:106:10: warning: 'bool spdlog::pattern_formatter::need_localtime_' [-Wreorder] 106 | bool need_localtime_; | ^~~~~~~~~~~~~~~ -make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/depend /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter-inl.h:1031:15: warning: when initialized here [-Wreorder] 1031 | SPDLOG_INLINE pattern_formatter::pattern_formatter(pattern_time_type time_type, std::string eol) | ^~~~~~~~~~~~~~~~~ +[ 65%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/testsource.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/testsource.cpp.o -MF CMakeFiles/makeinputs.dir/testsource.cpp.o.d -o CMakeFiles/makeinputs.dir/testsource.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastq-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fastq-load fastq-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-load.3.0.3 fastq-load.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-load.3 fastq-load +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 65%] Built target fastq-load +make -f tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 65%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o -MF CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o.d -o CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp +[ 65%] Linking C executable ../../../bin/sra-sort +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-sort.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-sort.dir/caps.c.o" "CMakeFiles/sra-sort.dir/mem.c.o" "CMakeFiles/sra-sort.dir/membank.c.o" "CMakeFiles/sra-sort.dir/paged-membank.c.o" "CMakeFiles/sra-sort.dir/paged-mmapbank.c.o" "CMakeFiles/sra-sort.dir/except.c.o" "CMakeFiles/sra-sort.dir/idx-mapping.c.o" "CMakeFiles/sra-sort.dir/map-file.c.o" "CMakeFiles/sra-sort.dir/col-pair.c.o" "CMakeFiles/sra-sort.dir/row-set.c.o" "CMakeFiles/sra-sort.dir/simple-row-set.c.o" "CMakeFiles/sra-sort.dir/mapping-row-set.c.o" "CMakeFiles/sra-sort.dir/sorting-row-set.c.o" "CMakeFiles/sra-sort.dir/meta-pair.c.o" "CMakeFiles/sra-sort.dir/dir-pair.c.o" "CMakeFiles/sra-sort.dir/tbl-pair.c.o" "CMakeFiles/sra-sort.dir/db-pair.c.o" "CMakeFiles/sra-sort.dir/glob-poslen.c.o" "CMakeFiles/sra-sort.dir/poslen-col-pair.c.o" "CMakeFiles/sra-sort.dir/ref-alignid-col.c.o" "CMakeFiles/sra-sort.dir/buff-writer.c.o" "CMakeFiles/sra-sort.dir/id-mapper-col.c.o" "CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o" "CMakeFiles/sra-sort.dir/run.c.o" "CMakeFiles/sra-sort.dir/sra-sort.c.o" "CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o" "CMakeFiles/sra-sort.dir/csra-tbl.c.o" "CMakeFiles/sra-sort.dir/csra-pair.c.o" -o ../../../bin/sra-sort /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -lbz2 -llzma +[ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o -MF CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o.d -o CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/capture-first-half-aligned.c +/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/run-source.cpp: In constructor 'data_sources::data_sources(const CommandLine&, const Arguments&, bool)': +/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/run-source.cpp:480:16: warning: unused variable 'havePerm' [-Wunused-variable] + 480 | auto const havePerm = perm != nullptr; + | ^~~~~~~~ +[ 65%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o -MF CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o.d -o CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pacbio-fmt.c +[ 65%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-illumina.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-illumina.c.o -MF CMakeFiles/srf-load.dir/srf-illumina.c.o.d -o CMakeFiles/srf-load.dir/srf-illumina.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-illumina.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-sort.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-sort sra-sort.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort.3.0.3 sra-sort.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort.3 sra-sort +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/run.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/run.c.o -MF CMakeFiles/sra-sort-cg.dir/run.c.o.d -o CMakeFiles/sra-sort-cg.dir/run.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/run.c +[ 65%] Built target sra-sort +make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-tag-lfr.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-tag-lfr.c.o -MF CMakeFiles/cg-load.dir/factory-tag-lfr.c.o.d -o CMakeFiles/cg-load.dir/factory-tag-lfr.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-tag-lfr.c +[ 65%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o -MF CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o.d -o CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp +[ 65%] Linking C executable ../../../bin/pacbio-loadxml +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/pacbio-loadxml.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/pacbio-loadxml.dir/pstring.c.o" "CMakeFiles/pacbio-loadxml.dir/common-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/run-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/loader-file.c.o" "CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o" "CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o" "CMakeFiles/pacbio-loadxml.dir/loader.c.o" "CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o" -o ../../../bin/pacbio-loadxml ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so +/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp: In function 'void run(const char*, bool, const int32_t*, const int32_t*, const int8_t*, int)': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp:76:16: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] + 76 | delete gw; + | ^~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp:45:20: note: 'gw' was declared here + 45 | GeneralWriter *gw; + | ^~ +[ 65%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-progress.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-progress.c.o -MF CMakeFiles/pacbio-load.dir/pl-progress.c.o.d -o CMakeFiles/pacbio-load.dir/pl-progress.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-progress.c +[ 65%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pacbio-load.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pacbio-load.c.o -MF CMakeFiles/pacbio-load.dir/pacbio-load.c.o.d -o CMakeFiles/pacbio-load.dir/pacbio-load.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pacbio-load.c +/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pacbio-load.c: In function 'pacbio_meta_entry': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pacbio-load.c:219:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 219 | rc = KLoaderMeta_Write( node, toolname, __DATE__, "PacBio HDF5", KAppVersion() ); + | ^~~~~~~~ +[ 65%] Linking CXX executable ../../../../../test-bin/bio-end-makeinputs +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/bio-end-makeinputs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o" -o ../../../../../test-bin/bio-end-makeinputs ../../../../../ilib/libgeneral-writer.a +[ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sra-sort.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sra-sort.c.o -MF CMakeFiles/sra-sort-cg.dir/sra-sort.c.o.d -o CMakeFiles/sra-sort-cg.dir/sra-sort.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sra-sort.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 65%] Built target bio-end-makeinputs +make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 63%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o +[ 65%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o -MF CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o.d -o CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/checklookup.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastq-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fastq-load fastq-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-load.3.0.3 fastq-load.3 -[ 63%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-absolid.c.o +[ 66%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o -MF CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o.d -o CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/xcheck-ref-align.c +[ 66%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-absolid.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-absolid.c.o -MF CMakeFiles/srf-load.dir/writer-absolid.c.o.d -o CMakeFiles/srf-load.dir/writer-absolid.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-absolid.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-load.3 fastq-load +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-loadxml.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-loadxml pacbio-loadxml.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-loadxml.3.0.3 pacbio-loadxml.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-loadxml.3 pacbio-loadxml make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 63%] Built target fastq-load +[ 66%] Built target pacbio-loadxml make -f tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/build.make tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-lock /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/DependInfo.cmake --color= -[ 63%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_3.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_3.c.o -MF CMakeFiles/cg-load.dir/f1_3.c.o.d -o CMakeFiles/cg-load.dir/f1_3.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_3.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/build.make tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 64%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o -MF CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o.d -o CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/xcheck-ref-align.c -[ 64%] Building C object tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/vdb-lock.c.o +[ 66%] Building C object tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/vdb-lock.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-lock\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/vdb-lock.c.o -MF CMakeFiles/vdb-lock.dir/vdb-lock.c.o.d -o CMakeFiles/vdb-lock.dir/vdb-lock.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-lock/vdb-lock.c -[ 64%] Linking C executable ../../../bin/pacbio-load -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/pacbio-load.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o" "CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o" "CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o" "CMakeFiles/pacbio-load.dir/pl-context.c.o" "CMakeFiles/pacbio-load.dir/pl-tools.c.o" "CMakeFiles/pacbio-load.dir/pl-zmw.c.o" "CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o" "CMakeFiles/pacbio-load.dir/pl-sequence.c.o" "CMakeFiles/pacbio-load.dir/pl-consensus.c.o" "CMakeFiles/pacbio-load.dir/pl-passes.c.o" "CMakeFiles/pacbio-load.dir/pl-metrics.c.o" "CMakeFiles/pacbio-load.dir/pl-regions.c.o" "CMakeFiles/pacbio-load.dir/pl-progress.c.o" "CMakeFiles/pacbio-load.dir/pacbio-load.c.o" -o ../../../bin/pacbio-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libsz.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libdl.a -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -[ 64%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_5.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_5.c.o -MF CMakeFiles/cg-load.dir/f1_5.c.o.d -o CMakeFiles/cg-load.dir/f1_5.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_5.c -[ 64%] Linking C executable ../../../bin/vdb-lock +[ 66%] Linking C executable ../../../bin/vdb-lock cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-lock.dir/link.txt --verbose=1 -[ 65%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/illumina-fmt.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/illumina-fmt.c.o -MF CMakeFiles/illumina-load.dir/illumina-fmt.c.o.d -o CMakeFiles/illumina-load.dir/illumina-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/illumina-fmt.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-lock.dir/vdb-lock.c.o" -o ../../../bin/vdb-lock /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -[ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o -MF CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o.d -o CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-tbl.c -[ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_7.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_7.c.o -MF CMakeFiles/cg-load.dir/f1_7.c.o.d -o CMakeFiles/cg-load.dir/f1_7.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_7.c +[ 66%] Linking CXX executable ../../../../test-bin/test-gw-dumper +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-gw-dumper.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o" -o ../../../../test-bin/test-gw-dumper ../../../../ilib/libgeneral-writer.a +[ 66%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_3.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_3.c.o -MF CMakeFiles/cg-load.dir/f1_3.c.o.d -o CMakeFiles/cg-load.dir/f1_3.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_3.c +[ 66%] Linking C executable ../../../bin/pacbio-load +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/pacbio-load.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o" "CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o" "CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o" "CMakeFiles/pacbio-load.dir/pl-context.c.o" "CMakeFiles/pacbio-load.dir/pl-tools.c.o" "CMakeFiles/pacbio-load.dir/pl-zmw.c.o" "CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o" "CMakeFiles/pacbio-load.dir/pl-sequence.c.o" "CMakeFiles/pacbio-load.dir/pl-consensus.c.o" "CMakeFiles/pacbio-load.dir/pl-passes.c.o" "CMakeFiles/pacbio-load.dir/pl-metrics.c.o" "CMakeFiles/pacbio-load.dir/pl-regions.c.o" "CMakeFiles/pacbio-load.dir/pl-progress.c.o" "CMakeFiles/pacbio-load.dir/pacbio-load.c.o" -o ../../../bin/pacbio-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libsz.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libdl.a -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-lock.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-lock vdb-lock.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-lock.3.0.3 vdb-lock.3 -[ 65%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-absolid.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-absolid.c.o -MF CMakeFiles/srf-load.dir/ztr-absolid.c.o.d -o CMakeFiles/srf-load.dir/ztr-absolid.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/ztr-absolid.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-lock.3 vdb-lock -/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp: In function 'void run(const char*, TestCaseType, const std::string*, int)': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:101:16: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] - 101 | delete gw; - | ^~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:54:20: note: 'gw' was declared here - 54 | GeneralWriter *gw; - | ^~ -In file included from /usr/include/c++/12/ios:40, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/sra-sdk-3.0.3+dfsg/libs/inc/general-writer/general-writer.hpp:34, - from /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:30: -In static member function 'static std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)', - inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:423:21, - inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:418:7, - inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy_chars(_CharT*, const _CharT*, const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:477:16, - inlined from 'void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::forward_iterator_tag) [with _FwdIterator = const char*; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.tcc:243:21, - inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:642:14, - inlined from 'void run(const char*, TestCaseType, const std::string*, int)' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:77:25: -/usr/include/c++/12/bits/char_traits.h:431:56: warning: 'db_schema' may be used uninitialized [-Wmaybe-uninitialized] - 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp: In function 'void run(const char*, TestCaseType, const std::string*, int)': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:57:21: note: 'db_schema' was declared here - 57 | const char* db_schema; - | ^~~~~~~~~ +[ 66%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o -MF CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o.d -o CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-tbl.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp: In function 'void run(const char*, bool, const int32_t*, const int32_t*, const int8_t*, int)': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp:76:16: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] - 76 | delete gw; - | ^~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp:45:20: note: 'gw' was declared here - 45 | GeneralWriter *gw; - | ^~ -[ 65%] Built target vdb-lock +[ 66%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_5.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_5.c.o -MF CMakeFiles/cg-load.dir/f1_5.c.o.d -o CMakeFiles/cg-load.dir/f1_5.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_5.c +[ 66%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-absolid.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-absolid.c.o -MF CMakeFiles/srf-load.dir/ztr-absolid.c.o.d -o CMakeFiles/srf-load.dir/ztr-absolid.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/ztr-absolid.c +[ 66%] Built target vdb-lock make -f tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/build.make tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-unlock /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/DependInfo.cmake --color= -[ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_0.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_0.c.o -MF CMakeFiles/cg-load.dir/f2_0.c.o.d -o CMakeFiles/cg-load.dir/f2_0.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_0.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/build.make tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 65%] Building C object tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o +[ 66%] Building C object tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-unlock\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o -MF CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o.d -o CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-unlock/vdb-unlock.c -/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/run-source.cpp: In constructor 'data_sources::data_sources(const CommandLine&, const Arguments&, bool)': -/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/run-source.cpp:480:16: warning: unused variable 'havePerm' [-Wunused-variable] - 480 | auto const havePerm = perm != nullptr; - | ^~~~~~~~ -[ 65%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/database-loader.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/database-loader.cpp.o -MF CMakeFiles/general-loader.dir/database-loader.cpp.o.d -o CMakeFiles/general-loader.dir/database-loader.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/database-loader.cpp -[ 65%] Linking CXX executable ../../../../test-bin/test-gw-dumper -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-gw-dumper.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-load pacbio-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-load.3.0.3 pacbio-load.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-load.3 pacbio-load -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o" -o ../../../../test-bin/test-gw-dumper ../../../../ilib/libgeneral-writer.a +[ 66%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_7.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_7.c.o -MF CMakeFiles/cg-load.dir/f1_7.c.o.d -o CMakeFiles/cg-load.dir/f1_7.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_7.c +[ 66%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_0.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_0.c.o -MF CMakeFiles/cg-load.dir/f2_0.c.o.d -o CMakeFiles/cg-load.dir/f2_0.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_0.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/database-loader.cpp:699:90: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 699 | rc = KLoaderMeta_WriteWithVersion ( node, m_programName.c_str(), __DATE__, KAppVersion(), m_softwareName.c_str(), m_softwareVersion ); - | ^~~~~~~~ -[ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_2.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_2.c.o -MF CMakeFiles/cg-load.dir/f2_2.c.o.d -o CMakeFiles/cg-load.dir/f2_2.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_2.c -[ 65%] Built target pacbio-load +[ 66%] Built target test-gw-dumper make -f tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/DependInfo.cmake --color= -[ 65%] Linking C executable ../../../bin/vdb-unlock -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-unlock.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/build -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o" -o ../../../bin/vdb-unlock /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 65%] Building C object tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o +[ 66%] Building C object tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/rd-filter-redact\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o -MF CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o.d -o CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/test-read-write-cursor.c -[ 65%] Linking CXX executable ../../../../../test-bin/bio-end-makeinputs -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/bio-end-makeinputs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o" -o ../../../../../test-bin/bio-end-makeinputs ../../../../../ilib/libgeneral-writer.a -[ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_4.c.o -[ 65%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-huffman.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_4.c.o -MF CMakeFiles/cg-load.dir/f2_4.c.o.d -o CMakeFiles/cg-load.dir/f2_4.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_4.c +[ 66%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_2.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_2.c.o -MF CMakeFiles/cg-load.dir/f2_2.c.o.d -o CMakeFiles/cg-load.dir/f2_2.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_2.c +[ 66%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-huffman.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-huffman.c.o -MF CMakeFiles/srf-load.dir/ztr-huffman.c.o.d -o CMakeFiles/srf-load.dir/ztr-huffman.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/ztr-huffman.c +[ 66%] Linking C executable ../../../bin/vdb-unlock +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-unlock.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o" -o ../../../bin/vdb-unlock /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +[ 66%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_4.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_4.c.o -MF CMakeFiles/cg-load.dir/f2_4.c.o.d -o CMakeFiles/cg-load.dir/f2_4.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_4.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-load pacbio-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-load.3.0.3 pacbio-load.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-load.3 pacbio-load cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-unlock.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-unlock vdb-unlock.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-unlock vdb-unlock.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-unlock.3.0.3 vdb-unlock.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-unlock.3 vdb-unlock -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 65%] Built target test-gw-dumper +[ 66%] Built target pacbio-load make -f tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/depend +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/DependInfo.cmake --color= -[ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-pair.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/csra-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/csra-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-pair.c -[ 65%] Built target vdb-unlock +[ 67%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_5.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_5.c.o -MF CMakeFiles/cg-load.dir/f2_5.c.o.d -o CMakeFiles/cg-load.dir/f2_5.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_5.c +[ 67%] Built target vdb-unlock make -f tools/internal/copycat/CMakeFiles/copycat.dir/build.make tools/internal/copycat/CMakeFiles/copycat.dir/depend -[ 65%] Linking C executable ../../../bin/illumina-load -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/illumina-load.dir/link.txt --verbose=1 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat/CMakeFiles/copycat.dir/DependInfo.cmake --color= -[ 66%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_5.c.o -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_5.c.o -MF CMakeFiles/cg-load.dir/f2_5.c.o.d -o CMakeFiles/cg-load.dir/f2_5.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_5.c -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/illumina-load.dir/pstring.c.o" "CMakeFiles/illumina-load.dir/common-xml.c.o" "CMakeFiles/illumina-load.dir/experiment-xml.c.o" "CMakeFiles/illumina-load.dir/run-xml.c.o" "CMakeFiles/illumina-load.dir/loader-file.c.o" "CMakeFiles/illumina-load.dir/loader-fmt.c.o" "CMakeFiles/illumina-load.dir/sra-writer.c.o" "CMakeFiles/illumina-load.dir/loader.c.o" "CMakeFiles/illumina-load.dir/writer-illumina.c.o" "CMakeFiles/illumina-load.dir/illumina-fmt.c.o" -o ../../../bin/illumina-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/copycat/CMakeFiles/copycat.dir/build.make tools/internal/copycat/CMakeFiles/copycat.dir/build -[ 66%] Building C object tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/rd-filter-redact\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o -MF CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o.d -o CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 66%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/copycat.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/copycat.c.o -MF CMakeFiles/copycat.dir/copycat.c.o.d -o CMakeFiles/copycat.dir/copycat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/copycat.c -[ 66%] Built target bio-end-makeinputs -[ 67%] Linking C executable ../../../bin/test-read-write-cursor -make -f tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build.make tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/depend -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-read-write-cursor.dir/link.txt --verbose=1 -[ 67%] Linking CXX executable ../../../../../test-bin/idx-text-makeinputs +[ 67%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/file.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/file.c.o -MF CMakeFiles/cg-load.dir/file.c.o.d -o CMakeFiles/cg-load.dir/file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/file.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/idx-text-makeinputs.dir/link.txt --verbose=1 -[ 67%] Linking C executable ../../../bin/sra-sort-cg -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-sort-cg.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o" -o ../../../bin/test-read-write-cursor /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-sort-cg.dir/caps.c.o" "CMakeFiles/sra-sort-cg.dir/mem.c.o" "CMakeFiles/sra-sort-cg.dir/membank.c.o" "CMakeFiles/sra-sort-cg.dir/paged-membank.c.o" "CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o" "CMakeFiles/sra-sort-cg.dir/except.c.o" "CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o" "CMakeFiles/sra-sort-cg.dir/map-file.c.o" "CMakeFiles/sra-sort-cg.dir/col-pair.c.o" "CMakeFiles/sra-sort-cg.dir/row-set.c.o" "CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/meta-pair.c.o" "CMakeFiles/sra-sort-cg.dir/dir-pair.c.o" "CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o" "CMakeFiles/sra-sort-cg.dir/db-pair.c.o" "CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o" "CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o" "CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o" "CMakeFiles/sra-sort-cg.dir/buff-writer.c.o" "CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o" "CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o" "CMakeFiles/sra-sort-cg.dir/run.c.o" "CMakeFiles/sra-sort-cg.dir/sra-sort.c.o" "CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o" "CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o" "CMakeFiles/sra-sort-cg.dir/csra-pair.c.o" -o ../../../bin/sra-sort-cg /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -lbz2 -llzma make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build.make tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o" -o ../../../../../test-bin/idx-text-makeinputs ../../../../../ilib/libgeneral-writer.a +make -f tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 67%] Building C object tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o +[ 67%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/copycat.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/rd-filter-redact\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o -MF CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o.d -o CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/copycat.c.o -MF CMakeFiles/copycat.dir/copycat.c.o.d -o CMakeFiles/copycat.dir/copycat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/copycat.c /build/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c: In function 'enter_date_name_vers': /build/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c:755:59: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 755 | rc = KMDataNodeWriteAttr ( node, "build", __DATE__ ); | ^~~~~~~~ -[ 67%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/context.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/context.c.o -MF CMakeFiles/vdb-copy.dir/context.c.o.d -o CMakeFiles/vdb-copy.dir/context.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/context.c -[ 67%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/file.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/file.c.o -MF CMakeFiles/cg-load.dir/file.c.o.d -o CMakeFiles/cg-load.dir/file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/file.c +[ 68%] Linking C executable ../../../bin/test-read-write-cursor +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-read-write-cursor.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o" -o ../../../bin/test-read-write-cursor /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +[ 68%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/file-version-factory.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/file-version-factory.c.o -MF CMakeFiles/cg-load.dir/file-version-factory.c.o.d -o CMakeFiles/cg-load.dir/file-version-factory.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/file-version-factory.c +[ 68%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-pair.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/csra-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/csra-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-pair.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-read-write-cursor.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv test-read-write-cursor test-read-write-cursor.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-read-write-cursor.3.0.3 test-read-write-cursor.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-sort-cg.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-read-write-cursor.3 test-read-write-cursor +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 68%] Built target test-read-write-cursor +make -f tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build.make tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build.make tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 68%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/context.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/context.c.o -MF CMakeFiles/vdb-copy.dir/context.c.o.d -o CMakeFiles/vdb-copy.dir/context.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/context.c +[ 68%] Linking C executable ../../../bin/sra-sort-cg +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-sort-cg.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-sort-cg.dir/caps.c.o" "CMakeFiles/sra-sort-cg.dir/mem.c.o" "CMakeFiles/sra-sort-cg.dir/membank.c.o" "CMakeFiles/sra-sort-cg.dir/paged-membank.c.o" "CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o" "CMakeFiles/sra-sort-cg.dir/except.c.o" "CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o" "CMakeFiles/sra-sort-cg.dir/map-file.c.o" "CMakeFiles/sra-sort-cg.dir/col-pair.c.o" "CMakeFiles/sra-sort-cg.dir/row-set.c.o" "CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/meta-pair.c.o" "CMakeFiles/sra-sort-cg.dir/dir-pair.c.o" "CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o" "CMakeFiles/sra-sort-cg.dir/db-pair.c.o" "CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o" "CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o" "CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o" "CMakeFiles/sra-sort-cg.dir/buff-writer.c.o" "CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o" "CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o" "CMakeFiles/sra-sort-cg.dir/run.c.o" "CMakeFiles/sra-sort-cg.dir/sra-sort.c.o" "CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o" "CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o" "CMakeFiles/sra-sort-cg.dir/csra-pair.c.o" -o ../../../bin/sra-sort-cg /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -lbz2 -llzma +[ 68%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/formats.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/formats.c.o -MF CMakeFiles/cg-load.dir/formats.c.o.d -o CMakeFiles/cg-load.dir/formats.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/formats.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-sort-cg.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-sort-cg sra-sort-cg.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort-cg.3.0.3 sra-sort-cg.3 -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort-cg.3 sra-sort-cg +[ 68%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccfileformat.c.o make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 67%] Built target test-read-write-cursor +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccfileformat.c.o -MF CMakeFiles/copycat.dir/ccfileformat.c.o.d -o CMakeFiles/copycat.dir/ccfileformat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccfileformat.c +[ 68%] Built target sra-sort-cg make -f tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/build.make tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/depend -[ 68%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/testsource.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/testsource.cpp.o -MF CMakeFiles/makeinputs.dir/testsource.cpp.o.d -o CMakeFiles/makeinputs.dir/testsource.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/DependInfo.cmake --color= -[ 68%] Built target sra-sort-cg -make -f tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build.make tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f illumina-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv illumina-load illumina-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-load.3.0.3 illumina-load.3 +[ 68%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-algn.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-algn.c.o -MF CMakeFiles/cg-load.dir/writer-algn.c.o.d -o CMakeFiles/cg-load.dir/writer-algn.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-algn.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/build.make tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-load.3 illumina-load -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build.make tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 68%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/namelist_tools.c.o -[ 68%] Building C object tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/make-read-filter.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/namelist_tools.c.o -MF CMakeFiles/vdb-diff.dir/namelist_tools.c.o.d -o CMakeFiles/vdb-diff.dir/namelist_tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/namelist_tools.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/make-read-filter.c.o -MF CMakeFiles/make-read-filter.dir/make-read-filter.c.o.d -o CMakeFiles/make-read-filter.dir/make-read-filter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c -[ 68%] Built target illumina-load -make -f tools/internal/align-cache/CMakeFiles/align-cache.dir/build.make tools/internal/align-cache/CMakeFiles/align-cache.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 68%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/helper.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/align-cache /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache/CMakeFiles/align-cache.dir/DependInfo.cmake --color= -[ 68%] Built target idx-text-makeinputs +/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp: In function 'void run(const char*, TestCaseType, const std::string*, int)': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:101:16: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] + 101 | delete gw; + | ^~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:54:20: note: 'gw' was declared here + 54 | GeneralWriter *gw; + | ^~ +In file included from /usr/include/c++/12/ios:40, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/sra-sdk-3.0.3+dfsg/libs/inc/general-writer/general-writer.hpp:34, + from /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:30: +In static member function 'static std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)', + inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:423:21, + inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:418:7, + inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy_chars(_CharT*, const _CharT*, const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:477:16, + inlined from 'void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::forward_iterator_tag) [with _FwdIterator = const char*; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.tcc:243:21, + inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:642:14, + inlined from 'void run(const char*, TestCaseType, const std::string*, int)' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:77:25: +/usr/include/c++/12/bits/char_traits.h:431:56: warning: 'db_schema' may be used uninitialized [-Wmaybe-uninitialized] + 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp: In function 'void run(const char*, TestCaseType, const std::string*, int)': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:57:21: note: 'db_schema' was declared here + 57 | const char* db_schema; + | ^~~~~~~~~ +[ 68%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-absolid.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-absolid.c.o -MF CMakeFiles/srf-load.dir/srf-absolid.c.o.d -o CMakeFiles/srf-load.dir/srf-absolid.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-absolid.c +[ 68%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cccat.c.o +[ 68%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o -MF CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o.d -o CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-evidence-dnbs.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cccat.c.o -MF CMakeFiles/copycat.dir/cccat.c.o.d -o CMakeFiles/copycat.dir/cccat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cccat.c +[ 69%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/coldefs.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/coldefs.c.o -MF CMakeFiles/vdb-diff.dir/coldefs.c.o.d -o CMakeFiles/vdb-diff.dir/coldefs.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/coldefs.c +[ 69%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/database-loader.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/database-loader.cpp.o -MF CMakeFiles/general-loader.dir/database-loader.cpp.o.d -o CMakeFiles/general-loader.dir/database-loader.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/database-loader.cpp +[ 69%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/helper.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/helper.c.o -MF CMakeFiles/vdb-copy.dir/helper.c.o.d -o CMakeFiles/vdb-copy.dir/helper.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/helper.c -make -f tools/internal/ccextract/CMakeFiles/ccextract.dir/build.make tools/internal/ccextract/CMakeFiles/ccextract.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/ccextract /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract/CMakeFiles/ccextract.dir/DependInfo.cmake --color= +[ 70%] Linking C executable ../../../bin/read-filter-redact +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cmake -E cmake_link_script CMakeFiles/read-filter-redact.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o" -o ../../../bin/read-filter-redact /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f read-filter-redact.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv read-filter-redact read-filter-redact.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s read-filter-redact.3.0.3 read-filter-redact.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s read-filter-redact.3 read-filter-redact make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/internal/align-cache/CMakeFiles/align-cache.dir/build.make tools/internal/align-cache/CMakeFiles/align-cache.dir/build +[ 70%] Built target read-filter-redact +make -f tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build.make tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/internal/ccextract/CMakeFiles/ccextract.dir/build.make tools/internal/ccextract/CMakeFiles/ccextract.dir/build -[ 68%] Building CXX object tools/internal/align-cache/CMakeFiles/align-cache.dir/align-cache.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/align-cache\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/internal/align-cache/CMakeFiles/align-cache.dir/align-cache.cpp.o -MF CMakeFiles/align-cache.dir/align-cache.cpp.o.d -o CMakeFiles/align-cache.dir/align-cache.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/align-cache/align-cache.cpp +make -f tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build.make tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/database-loader.cpp:699:90: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 699 | rc = KLoaderMeta_WriteWithVersion ( node, m_programName.c_str(), __DATE__, KAppVersion(), m_softwareName.c_str(), m_softwareVersion ); + | ^~~~~~~~ +[ 70%] Building C object tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/make-read-filter.c.o +[ 70%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/make-read-filter.c.o -MF CMakeFiles/make-read-filter.dir/make-read-filter.c.o.d -o CMakeFiles/make-read-filter.dir/make-read-filter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o -MF CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o.d -o CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-evidence-intervals.c +[ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o -MF CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o.d -o CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/vdb-diff-context.c In file included from /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:33: /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.h: In function 'rowCount': /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.h:124:16: warning: unused variable 'rc' [-Wunused-variable] 124 | rc_t const rc = VCursorIdRange(curs, cid, first, &count); | ^~ -[ 68%] Building C object tools/internal/ccextract/CMakeFiles/ccextract.dir/ccextract.c.o /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c: In function 'main_1': /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:598:9: warning: ignoring return value of 'chdir' declared with attribute 'warn_unused_result' [-Wunused-result] 598 | chdir(wd); | ^~~~~~~~~ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ccextract\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/ccextract/CMakeFiles/ccextract.dir/ccextract.c.o -MF CMakeFiles/ccextract.dir/ccextract.c.o.d -o CMakeFiles/ccextract.dir/ccextract.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/ccextract/ccextract.c /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c: In function 'temporaryDirectory': /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:938:5: warning: ignoring return value of 'mkdtemp' declared with attribute 'warn_unused_result' [-Wunused-result] 938 | mkdtemp(pattern); @@ -5437,270 +5481,342 @@ /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:692:13: warning: 'test' defined but not used [-Wunused-function] 692 | static void test(void) | ^~~~ -[ 68%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-absolid.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-absolid.c.o -MF CMakeFiles/srf-load.dir/srf-absolid.c.o.d -o CMakeFiles/srf-load.dir/srf-absolid.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-absolid.c -[ 69%] Linking C executable ../../../bin/read-filter-redact -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cmake -E cmake_link_script CMakeFiles/read-filter-redact.dir/link.txt --verbose=1 -[ 69%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/file-version-factory.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/file-version-factory.c.o -MF CMakeFiles/cg-load.dir/file-version-factory.c.o.d -o CMakeFiles/cg-load.dir/file-version-factory.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/file-version-factory.c -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o" -o ../../../bin/read-filter-redact /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -[ 69%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccfileformat.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccfileformat.c.o -MF CMakeFiles/copycat.dir/ccfileformat.c.o.d -o CMakeFiles/copycat.dir/ccfileformat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccfileformat.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f read-filter-redact.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv read-filter-redact read-filter-redact.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s read-filter-redact.3.0.3 read-filter-redact.3 -[ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/coldefs.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/coldefs.c.o -MF CMakeFiles/vdb-diff.dir/coldefs.c.o.d -o CMakeFiles/vdb-diff.dir/coldefs.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/coldefs.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s read-filter-redact.3 read-filter-redact +[ 70%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctree.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctree.c.o -MF CMakeFiles/copycat.dir/cctree.c.o.d -o CMakeFiles/copycat.dir/cctree.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctree.c +[ 70%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-seq.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-seq.c.o -MF CMakeFiles/cg-load.dir/writer-seq.c.o.d -o CMakeFiles/cg-load.dir/writer-seq.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-seq.c +[ 70%] Linking C executable ../../../bin/cg-load +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/cg-load.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/cg-load.dir/cg-load.c.o" "CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o" "CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o" "CMakeFiles/cg-load.dir/factory-mappings.c.o" "CMakeFiles/cg-load.dir/factory-reads.c.o" "CMakeFiles/cg-load.dir/factory-tag-lfr.c.o" "CMakeFiles/cg-load.dir/f1_3.c.o" "CMakeFiles/cg-load.dir/f1_5.c.o" "CMakeFiles/cg-load.dir/f1_7.c.o" "CMakeFiles/cg-load.dir/f2_0.c.o" "CMakeFiles/cg-load.dir/f2_2.c.o" "CMakeFiles/cg-load.dir/f2_4.c.o" "CMakeFiles/cg-load.dir/f2_5.c.o" "CMakeFiles/cg-load.dir/file.c.o" "CMakeFiles/cg-load.dir/file-version-factory.c.o" "CMakeFiles/cg-load.dir/formats.c.o" "CMakeFiles/cg-load.dir/writer-algn.c.o" "CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o" "CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o" "CMakeFiles/cg-load.dir/writer-seq.c.o" -o ../../../bin/cg-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f cg-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv cg-load cg-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cg-load.3.0.3 cg-load.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cg-load.3 cg-load make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 70%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/coldefs.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/coldefs.c.o -MF CMakeFiles/vdb-copy.dir/coldefs.c.o.d -o CMakeFiles/vdb-copy.dir/coldefs.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/coldefs.c -[ 70%] Built target read-filter-redact -make -f tools/internal/md5cp/CMakeFiles/md5cp.dir/build.make tools/internal/md5cp/CMakeFiles/md5cp.dir/depend +[ 70%] Built target cg-load +[ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/cmn.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/cmn.c.o -MF CMakeFiles/vdb-diff.dir/cmn.c.o.d -o CMakeFiles/vdb-diff.dir/cmn.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/cmn.c +make -f tools/internal/align-cache/CMakeFiles/align-cache.dir/build.make tools/internal/align-cache/CMakeFiles/align-cache.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/md5cp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp/CMakeFiles/md5cp.dir/DependInfo.cmake --color= +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/align-cache /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache 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-I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/formats.c.o -MF CMakeFiles/cg-load.dir/formats.c.o.d -o CMakeFiles/cg-load.dir/formats.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/formats.c -[ 70%] Building C object tools/internal/md5cp/CMakeFiles/md5cp.dir/md5cp.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/md5cp/CMakeFiles/md5cp.dir/md5cp.c.o -MF CMakeFiles/md5cp.dir/md5cp.c.o.d -o CMakeFiles/md5cp.dir/md5cp.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/md5cp/md5cp.c -[ 70%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cccat.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cccat.c.o -MF CMakeFiles/copycat.dir/cccat.c.o.d -o CMakeFiles/copycat.dir/cccat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cccat.c -[ 70%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-algn.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-algn.c.o -MF CMakeFiles/cg-load.dir/writer-algn.c.o.d -o CMakeFiles/cg-load.dir/writer-algn.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-algn.c -[ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o -MF CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o.d -o CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/vdb-diff-context.c +[ 70%] Building CXX object tools/internal/align-cache/CMakeFiles/align-cache.dir/align-cache.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/align-cache\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/internal/align-cache/CMakeFiles/align-cache.dir/align-cache.cpp.o -MF CMakeFiles/align-cache.dir/align-cache.cpp.o.d -o CMakeFiles/align-cache.dir/align-cache.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/align-cache/align-cache.cpp +[ 70%] Linking CXX executable ../../../../../test-bin/idx-text-makeinputs +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/idx-text-makeinputs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o" -o ../../../../../test-bin/idx-text-makeinputs ../../../../../ilib/libgeneral-writer.a +[ 70%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/coldefs.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/coldefs.c.o -MF CMakeFiles/vdb-copy.dir/coldefs.c.o.d -o CMakeFiles/vdb-copy.dir/coldefs.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/coldefs.c +[ 70%] Linking CXX executable ../../../../test-bin/makeinputs +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/makeinputs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/makeinputs.dir/makeinputs.cpp.o CMakeFiles/makeinputs.dir/testsource.cpp.o -o ../../../../test-bin/makeinputs ../../../../ilib/libgeneral-writer.a -lncbi-vdb +[ 70%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctree-dump.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctree-dump.c.o -MF CMakeFiles/copycat.dir/cctree-dump.c.o.d -o CMakeFiles/copycat.dir/cctree-dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctree-dump.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 70%] Built target makeinputs +[ 70%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctar.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctar.c.o -MF CMakeFiles/copycat.dir/cctar.c.o.d -o CMakeFiles/copycat.dir/cctar.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c +/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c: In function 'what_header_type': +/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c:1015:42: warning: the comparison will always evaluate as 'true' for the address of 'fullsize' will never be NULL [-Waddress] + 1015 | header->suntar.extcount && + | ^~ +/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c:598:25: note: 'fullsize' declared here + 598 | sun_fullsize fullsize; /* 502 non-conformant */ + | ^~~~~~~~ +[ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/row_by_row.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/row_by_row.c.o -MF CMakeFiles/vdb-diff.dir/row_by_row.c.o.d -o CMakeFiles/vdb-diff.dir/row_by_row.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/row_by_row.c [ 70%] Linking C executable ../../../bin/srf-load cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/srf-load.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/srf-load.dir/pstring.c.o" "CMakeFiles/srf-load.dir/common-xml.c.o" "CMakeFiles/srf-load.dir/experiment-xml.c.o" "CMakeFiles/srf-load.dir/run-xml.c.o" "CMakeFiles/srf-load.dir/loader-file.c.o" "CMakeFiles/srf-load.dir/loader-fmt.c.o" "CMakeFiles/srf-load.dir/sra-writer.c.o" "CMakeFiles/srf-load.dir/loader.c.o" "CMakeFiles/srf-load.dir/srf.c.o" "CMakeFiles/srf-load.dir/srf-fmt.c.o" "CMakeFiles/srf-load.dir/writer-illumina.c.o" "CMakeFiles/srf-load.dir/ztr-illumina.c.o" "CMakeFiles/srf-load.dir/srf-illumina.c.o" "CMakeFiles/srf-load.dir/writer-absolid.c.o" "CMakeFiles/srf-load.dir/ztr-absolid.c.o" "CMakeFiles/srf-load.dir/ztr-huffman.c.o" "CMakeFiles/srf-load.dir/srf-absolid.c.o" -o ../../../bin/srf-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so -[ 70%] Linking C executable ../../../bin/ccextract -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract && /usr/bin/cmake -E cmake_link_script CMakeFiles/ccextract.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/ccextract.dir/ccextract.c.o -o ../../../bin/ccextract /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libxml2.so -[ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/cmn.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/cmn.c.o -MF CMakeFiles/vdb-diff.dir/cmn.c.o.d -o CMakeFiles/vdb-diff.dir/cmn.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/cmn.c +[ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/col_by_col.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/col_by_col.c.o -MF CMakeFiles/vdb-diff.dir/col_by_col.c.o.d -o CMakeFiles/vdb-diff.dir/col_by_col.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/col_by_col.c +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f srf-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv srf-load srf-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srf-load.3.0.3 srf-load.3 +[ 70%] Built target idx-text-makeinputs cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srf-load.3 srf-load +make -f tools/internal/ccextract/CMakeFiles/ccextract.dir/build.make tools/internal/ccextract/CMakeFiles/ccextract.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/ccextract /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract/CMakeFiles/ccextract.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 70%] Linking C executable ../../../bin/md5cp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp && /usr/bin/cmake -E cmake_link_script CMakeFiles/md5cp.dir/link.txt --verbose=1 +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/internal/ccextract/CMakeFiles/ccextract.dir/build.make tools/internal/ccextract/CMakeFiles/ccextract.dir/build [ 70%] Built target srf-load +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/internal/md5cp/CMakeFiles/md5cp.dir/build.make tools/internal/md5cp/CMakeFiles/md5cp.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/md5cp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp/CMakeFiles/md5cp.dir/DependInfo.cmake --color= +[ 70%] Building C object tools/internal/ccextract/CMakeFiles/ccextract.dir/ccextract.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE 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tools/internal/md5cp/CMakeFiles/md5cp.dir/md5cp.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/md5cp/CMakeFiles/md5cp.dir/md5cp.c.o -MF CMakeFiles/md5cp.dir/md5cp.c.o.d -o CMakeFiles/md5cp.dir/md5cp.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/md5cp/md5cp.c +[ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff.c.o -MF CMakeFiles/vdb-diff.dir/vdb-diff.c.o.d -o CMakeFiles/vdb-diff.dir/vdb-diff.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/vdb-diff.c +[ 70%] Linking C executable ../../../bin/make-read-filter +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/make-read-filter.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/make-read-filter.dir/make-read-filter.c.o" -o ../../../bin/make-read-filter /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +[ 70%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/get_platform.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/get_platform.c.o -MF CMakeFiles/vdb-copy.dir/get_platform.c.o.d -o CMakeFiles/vdb-copy.dir/get_platform.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/get_platform.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f make-read-filter.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv make-read-filter make-read-filter.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s make-read-filter.3.0.3 make-read-filter.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s make-read-filter.3 make-read-filter +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 70%] Built target make-read-filter +[ 71%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccsra.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccsra.c.o -MF CMakeFiles/copycat.dir/ccsra.c.o.d -o CMakeFiles/copycat.dir/ccsra.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccsra.c +[ 71%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/namelist_tools.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/namelist_tools.c.o -MF CMakeFiles/vdb-copy.dir/namelist_tools.c.o.d -o CMakeFiles/vdb-copy.dir/namelist_tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/namelist_tools.c +[ 71%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccsubchunk.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccsubchunk.c.o -MF CMakeFiles/copycat.dir/ccsubchunk.c.o.d -o CMakeFiles/copycat.dir/ccsubchunk.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccsubchunk.c +[ 71%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/copy_meta.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/copy_meta.c.o -MF CMakeFiles/vdb-copy.dir/copy_meta.c.o.d -o CMakeFiles/vdb-copy.dir/copy_meta.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c +[ 71%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccfile.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccfile.c.o -MF CMakeFiles/copycat.dir/ccfile.c.o.d -o CMakeFiles/copycat.dir/ccfile.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccfile.c +/build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c: In function 'enter_date_name_vers': +/build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c:349:59: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 349 | rc = KMDataNodeWriteAttr ( node, "build", __DATE__ ); + | ^~~~~~~~ +[ 71%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/fileformat.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/fileformat.c.o -MF CMakeFiles/copycat.dir/kff/fileformat.c.o.d -o CMakeFiles/copycat.dir/kff/fileformat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/fileformat.c +[ 71%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffext.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffext.c.o -MF CMakeFiles/copycat.dir/kff/ffext.c.o.d -o CMakeFiles/copycat.dir/kff/ffext.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffext.c +[ 71%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/type_matcher.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/type_matcher.c.o -MF CMakeFiles/vdb-copy.dir/type_matcher.c.o.d -o CMakeFiles/vdb-copy.dir/type_matcher.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/type_matcher.c +[ 71%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffkey.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffkey.c.o -MF CMakeFiles/copycat.dir/kff/ffkey.c.o.d -o CMakeFiles/copycat.dir/kff/ffkey.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffkey.c +[ 71%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffmagic.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffmagic.c.o -MF CMakeFiles/copycat.dir/kff/ffmagic.c.o.d -o CMakeFiles/copycat.dir/kff/ffmagic.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffmagic.c +[ 71%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/proc.cpp.o -MF CMakeFiles/sratools.dir/proc.cpp.o.d -o CMakeFiles/sratools.dir/proc.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.cpp +[ 71%] Building CXX object tools/internal/align-cache/CMakeFiles/align-cache.dir/helper.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/align-cache\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/internal/align-cache/CMakeFiles/align-cache.dir/helper.cpp.o -MF CMakeFiles/align-cache.dir/helper.cpp.o.d -o CMakeFiles/align-cache.dir/helper.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/align-cache/helper.cpp +[ 71%] Linking C executable ../../../bin/vdb-diff +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-diff.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-diff.dir/namelist_tools.c.o" "CMakeFiles/vdb-diff.dir/coldefs.c.o" "CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o" "CMakeFiles/vdb-diff.dir/cmn.c.o" "CMakeFiles/vdb-diff.dir/row_by_row.c.o" "CMakeFiles/vdb-diff.dir/col_by_col.c.o" "CMakeFiles/vdb-diff.dir/vdb-diff.c.o" -o ../../../bin/vdb-diff /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-diff.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-diff vdb-diff.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-diff.3.0.3 vdb-diff.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-diff.3 vdb-diff +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 71%] Built target vdb-diff make -f tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/build.make tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-cmp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/DependInfo.cmake --color= -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/md5cp.dir/md5cp.c.o -o ../../../bin/md5cp /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/row_by_row.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/row_by_row.c.o -MF CMakeFiles/vdb-diff.dir/row_by_row.c.o.d -o CMakeFiles/vdb-diff.dir/row_by_row.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/row_by_row.c +[ 71%] Linking C executable ../../../bin/ccextract +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract && /usr/bin/cmake -E cmake_link_script CMakeFiles/ccextract.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/build.make tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 70%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/get_platform.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/get_platform.c.o -MF CMakeFiles/vdb-copy.dir/get_platform.c.o.d -o CMakeFiles/vdb-copy.dir/get_platform.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/get_platform.c -[ 70%] Building C object tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/meta-cmp.c.o +[ 71%] Building C object tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/meta-cmp.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/meta-cmp\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/meta-cmp.c.o -MF CMakeFiles/meta-cmp.dir/meta-cmp.c.o.d -o CMakeFiles/meta-cmp.dir/meta-cmp.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-cmp/meta-cmp.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f ccextract.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv ccextract ccextract.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ccextract.3.0.3 ccextract.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ccextract.3 ccextract -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/ccextract.dir/ccextract.c.o -o ../../../bin/ccextract /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libxml2.so +[ 71%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/uuid.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/uuid.cpp.o -MF CMakeFiles/sratools.dir/uuid.cpp.o.d -o CMakeFiles/sratools.dir/uuid.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/uuid.cpp +[ 72%] Linking CXX executable ../../../../../test-bin/idx-text-checklookup +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/idx-text-checklookup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o" -o ../../../../../test-bin/idx-text-checklookup /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 72%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/accession.cpp.o +cd 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CMakeFiles/md5cp.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/md5cp.dir/md5cp.c.o -o ../../../bin/md5cp /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f md5cp.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv md5cp md5cp.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s md5cp.3.0.3 md5cp.3 -[ 70%] Building CXX object tools/internal/align-cache/CMakeFiles/align-cache.dir/helper.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/align-cache\" -Dx86_64 -I/usr/include/ncbi-vdb 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'/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy/CMakeFiles/meta-copy.dir/DependInfo.cmake --color= -[ 70%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/namelist_tools.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/namelist_tools.c.o -MF CMakeFiles/vdb-copy.dir/namelist_tools.c.o.d -o CMakeFiles/vdb-copy.dir/namelist_tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/namelist_tools.c -[ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/col_by_col.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/col_by_col.c.o -MF CMakeFiles/vdb-diff.dir/col_by_col.c.o.d -o CMakeFiles/vdb-diff.dir/col_by_col.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/col_by_col.c -[ 70%] Built target md5cp -make -f tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build.make tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/crc32sum /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build.make tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 70%] Linking C executable ../../../bin/meta-cmp -[ 70%] Building C object tools/internal/meta-copy/CMakeFiles/meta-copy.dir/meta-copy.c.o +[ 72%] Built target md5cp +[ 73%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/redactval.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/redactval.c.o -MF CMakeFiles/vdb-copy.dir/redactval.c.o.d -o CMakeFiles/vdb-copy.dir/redactval.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/redactval.c +[ 73%] Linking C executable ../../../bin/meta-cmp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp && /usr/bin/cmake -E cmake_link_script CMakeFiles/meta-cmp.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/meta-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/meta-copy/CMakeFiles/meta-copy.dir/meta-copy.c.o -MF CMakeFiles/meta-copy.dir/meta-copy.c.o.d -o CMakeFiles/meta-copy.dir/meta-copy.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build.make tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build -[ 70%] Linking C executable ../../../bin/make-read-filter -[ 70%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/make-read-filter.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o -MF CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o.d -o CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-evidence-dnbs.c -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 73%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/config_values.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/config_values.c.o -MF CMakeFiles/vdb-copy.dir/config_values.c.o.d -o CMakeFiles/vdb-copy.dir/config_values.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/config_values.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/meta-cmp.dir/meta-cmp.c.o" -o ../../../bin/meta-cmp /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/make-read-filter.dir/make-read-filter.c.o" -o ../../../bin/make-read-filter /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -[ 71%] Building C object tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/crc32sum.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/crc32sum.c.o -MF CMakeFiles/crc32sum.dir/crc32sum.c.o.d -o CMakeFiles/crc32sum.dir/crc32sum.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/crc32sum/crc32sum.c -/build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c: In function 'KMain': -/build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c:330:23: warning: unused variable 'diffs' [-Wunused-variable] - 330 | unsigned long int diffs = 0; - | ^~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c: At top level: -/build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c:186:13: warning: 'cleanup_rc' defined but not used [-Wunused-function] - 186 | static void cleanup_rc( void ) { - | ^~~~~~~~~~ -[ 71%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff.c.o -MF CMakeFiles/vdb-diff.dir/vdb-diff.c.o.d -o CMakeFiles/vdb-diff.dir/vdb-diff.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/vdb-diff.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f meta-cmp.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv meta-cmp meta-cmp.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-cmp.3.0.3 meta-cmp.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-cmp.3 meta-cmp +[ 73%] Linking C executable ../../../bin/copycat make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f make-read-filter.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv make-read-filter make-read-filter.3.0.3 -[ 71%] Built target meta-cmp -[ 71%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctree.c.o -make -f tools/test-tools/test-download/CMakeFiles/test-download.dir/build.make tools/test-tools/test-download/CMakeFiles/test-download.dir/depend -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctree.c.o -MF CMakeFiles/copycat.dir/cctree.c.o.d -o CMakeFiles/copycat.dir/cctree.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctree.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s make-read-filter.3.0.3 make-read-filter.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cmake -E cmake_link_script CMakeFiles/copycat.dir/link.txt --verbose=1 +[ 73%] Built target meta-cmp +make -f tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build.make tools/internal/meta-copy/CMakeFiles/meta-copy.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/test-download /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download/CMakeFiles/test-download.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s make-read-filter.3 make-read-filter +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy/CMakeFiles/meta-copy.dir/DependInfo.cmake --color= +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/copycat.dir/copycat.c.o CMakeFiles/copycat.dir/ccfileformat.c.o CMakeFiles/copycat.dir/cccat.c.o CMakeFiles/copycat.dir/cctree.c.o "CMakeFiles/copycat.dir/cctree-dump.c.o" CMakeFiles/copycat.dir/cctar.c.o CMakeFiles/copycat.dir/ccsra.c.o CMakeFiles/copycat.dir/ccsubchunk.c.o CMakeFiles/copycat.dir/ccfile.c.o CMakeFiles/copycat.dir/kff/fileformat.c.o CMakeFiles/copycat.dir/kff/ffext.c.o CMakeFiles/copycat.dir/kff/ffkey.c.o CMakeFiles/copycat.dir/kff/ffmagic.c.o -o ../../../bin/copycat /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libmagic.so make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 71%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/copy_meta.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/copy_meta.c.o -MF CMakeFiles/vdb-copy.dir/copy_meta.c.o.d -o CMakeFiles/vdb-copy.dir/copy_meta.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/test-tools/test-download/CMakeFiles/test-download.dir/build.make tools/test-tools/test-download/CMakeFiles/test-download.dir/build +make -f tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build.make tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build +[ 73%] Built target idx-text-checklookup make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 71%] Built target make-read-filter -make -f tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build.make tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/depend -[ 71%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o -MF CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o.d -o CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-evidence-intervals.c +make -f tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build.make tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/depend +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f copycat.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f ccextract.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv copycat copycat.3.0.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/kdb-index /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/DependInfo.cmake --color= -[ 72%] Building C object tools/test-tools/test-download/CMakeFiles/test-download.dir/test-download.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/test-download/CMakeFiles/test-download.dir/test-download.c.o -MF CMakeFiles/test-download.dir/test-download.c.o.d -o CMakeFiles/test-download.dir/test-download.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/test-download/test-download.c -[ 72%] Linking C executable ../../../bin/crc32sum -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum && /usr/bin/cmake -E cmake_link_script CMakeFiles/crc32sum.dir/link.txt --verbose=1 -[ 72%] Linking C executable ../../../bin/meta-copy +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/crc32sum /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/DependInfo.cmake --color= +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s copycat.3.0.3 copycat.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv ccextract ccextract.3.0.3 +[ 73%] Building C object tools/internal/meta-copy/CMakeFiles/meta-copy.dir/meta-copy.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ccextract.3.0.3 ccextract.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/meta-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/meta-copy/CMakeFiles/meta-copy.dir/meta-copy.c.o -MF CMakeFiles/meta-copy.dir/meta-copy.c.o.d -o CMakeFiles/meta-copy.dir/meta-copy.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s copycat.3 copycat +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ccextract.3 ccextract make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build.make tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy && /usr/bin/cmake -E cmake_link_script CMakeFiles/meta-copy.dir/link.txt --verbose=1 +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build.make tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c: In function 'enter_date_name_vers': -/build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c:349:59: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 349 | rc = KMDataNodeWriteAttr ( node, "build", __DATE__ ); - | ^~~~~~~~ +[ 73%] Built target copycat +make -f tools/test-tools/test-download/CMakeFiles/test-download.dir/build.make tools/test-tools/test-download/CMakeFiles/test-download.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/test-download /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download/CMakeFiles/test-download.dir/DependInfo.cmake --color= +[ 74%] Building C object tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/crc32sum.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/crc32sum.c.o -MF CMakeFiles/crc32sum.dir/crc32sum.c.o.d -o CMakeFiles/crc32sum.dir/crc32sum.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/crc32sum/crc32sum.c +[ 74%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/vdb-copy.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/vdb-copy.c.o -MF CMakeFiles/vdb-copy.dir/vdb-copy.c.o.d -o CMakeFiles/vdb-copy.dir/vdb-copy.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/vdb-copy.c +[ 74%] Linking C executable ../../../bin/crc32sum +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum && /usr/bin/cmake -E cmake_link_script CMakeFiles/crc32sum.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/crc32sum.dir/crc32sum.c.o -o ../../../bin/crc32sum /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/meta-copy.dir/meta-copy.c.o" -o ../../../bin/meta-copy /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -[ 72%] Building C object tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/kdb-index.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/kdb-index.c.o -MF CMakeFiles/kdb-index.dir/kdb-index.c.o.d -o CMakeFiles/kdb-index.dir/kdb-index.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/kdb-index/kdb-index.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f meta-copy.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f crc32sum.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv meta-copy meta-copy.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv crc32sum crc32sum.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-copy.3.0.3 meta-copy.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-copy.3 meta-copy cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s crc32sum.3.0.3 crc32sum.3 -[ 72%] Linking C executable ../../../bin/vdb-diff -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-diff.dir/link.txt --verbose=1 -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s crc32sum.3 crc32sum make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 72%] Built target meta-copy -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-diff.dir/namelist_tools.c.o" "CMakeFiles/vdb-diff.dir/coldefs.c.o" "CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o" "CMakeFiles/vdb-diff.dir/cmn.c.o" "CMakeFiles/vdb-diff.dir/row_by_row.c.o" "CMakeFiles/vdb-diff.dir/col_by_col.c.o" "CMakeFiles/vdb-diff.dir/vdb-diff.c.o" -o ../../../bin/vdb-diff /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 72%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-seq.c.o -make -f tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/build.make tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/depend -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-seq.c.o -MF CMakeFiles/cg-load.dir/writer-seq.c.o.d -o CMakeFiles/cg-load.dir/writer-seq.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-seq.c -[ 73%] Linking C executable ../../../bin/kdb-index +[ 74%] Built target crc32sum +make -f tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build.make tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pacbio-correct /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/DependInfo.cmake --color= +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/kdb-index /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build.make tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 74%] Building C object tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/kdb-index.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/kdb-index.c.o -MF CMakeFiles/kdb-index.dir/kdb-index.c.o.d -o CMakeFiles/kdb-index.dir/kdb-index.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/kdb-index/kdb-index.c +[ 74%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o -MF CMakeFiles/sratools.dir/service.cpp.o.d -o CMakeFiles/sratools.dir/service.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/service.cpp +[ 75%] Linking C executable ../../../bin/kdb-index cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index && /usr/bin/cmake -E cmake_link_script CMakeFiles/kdb-index.dir/link.txt --verbose=1 -[ 73%] Built target crc32sum -[ 73%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctree-dump.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctree-dump.c.o -MF CMakeFiles/copycat.dir/cctree-dump.c.o.d -o CMakeFiles/copycat.dir/cctree-dump.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctree-dump.c -[ 74%] Linking CXX executable ../../../../../test-bin/idx-text-checklookup +[ 75%] Built target ccextract +make -f tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/build.make tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/depend /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/kdb-index.dir/kdb-index.c.o" -o ../../../bin/kdb-index /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -make -f tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/build.make tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/depend -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/idx-text-checklookup.dir/link.txt --verbose=1 +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/test-tools/test-download/CMakeFiles/test-download.dir/build.make tools/test-tools/test-download/CMakeFiles/test-download.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/schema-replace /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/schema-replace /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/DependInfo.cmake --color= +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pacbio-correct /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c: In function 'KMain': +/build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c:330:23: warning: unused variable 'diffs' [-Wunused-variable] + 330 | unsigned long int diffs = 0; + | ^~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c: At top level: +/build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c:186:13: warning: 'cleanup_rc' defined but not used [-Wunused-function] + 186 | static void cleanup_rc( void ) { + | ^~~~~~~~~~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/build.make tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/build +[ 76%] Building C object tools/test-tools/test-download/CMakeFiles/test-download.dir/test-download.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/test-download/CMakeFiles/test-download.dir/test-download.c.o -MF CMakeFiles/test-download.dir/test-download.c.o.d -o CMakeFiles/test-download.dir/test-download.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/test-download/test-download.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o" -o ../../../../../test-bin/idx-text-checklookup /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 74%] Building C object tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 74%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/type_matcher.c.o -make -f tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/build.make tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/build +[ 76%] Building C object tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o -MF CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o.d -o CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pacbio-correct/pacbio-correct.c -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/type_matcher.c.o -MF CMakeFiles/vdb-copy.dir/type_matcher.c.o.d -o CMakeFiles/vdb-copy.dir/type_matcher.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/type_matcher.c -[ 74%] Building C object tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/schema-replace.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/schema-replace && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/schema-replace.c.o -MF CMakeFiles/schema-replace.dir/schema-replace.c.o.d -o CMakeFiles/schema-replace.dir/schema-replace.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/schema-replace/schema-replace.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-diff.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-diff vdb-diff.3.0.3 -[ 74%] Linking C executable ../../../bin/cg-load -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-diff.3.0.3 vdb-diff.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/cg-load.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-diff.3 vdb-diff -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/cg-load.dir/cg-load.c.o" "CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o" "CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o" "CMakeFiles/cg-load.dir/factory-mappings.c.o" "CMakeFiles/cg-load.dir/factory-reads.c.o" "CMakeFiles/cg-load.dir/factory-tag-lfr.c.o" "CMakeFiles/cg-load.dir/f1_3.c.o" "CMakeFiles/cg-load.dir/f1_5.c.o" "CMakeFiles/cg-load.dir/f1_7.c.o" "CMakeFiles/cg-load.dir/f2_0.c.o" "CMakeFiles/cg-load.dir/f2_2.c.o" "CMakeFiles/cg-load.dir/f2_4.c.o" "CMakeFiles/cg-load.dir/f2_5.c.o" "CMakeFiles/cg-load.dir/file.c.o" "CMakeFiles/cg-load.dir/file-version-factory.c.o" "CMakeFiles/cg-load.dir/formats.c.o" "CMakeFiles/cg-load.dir/writer-algn.c.o" "CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o" "CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o" "CMakeFiles/cg-load.dir/writer-seq.c.o" -o ../../../bin/cg-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kdb-index.3.0.3 -[ 74%] Built target vdb-diff -make -f tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/build.make tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/sortreadtest /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest 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tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/schema-replace.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/schema-replace && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/schema-replace.c.o -MF CMakeFiles/schema-replace.dir/schema-replace.c.o.d -o CMakeFiles/schema-replace.dir/schema-replace.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/schema-replace/schema-replace.c +[ 76%] Linking C executable ../../../bin/meta-copy +cd 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-I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/json-parse.cpp.o -MF CMakeFiles/sratools.dir/json-parse.cpp.o.d -o CMakeFiles/sratools.dir/json-parse.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/json-parse.cpp +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-copy.dir/context.c.o" "CMakeFiles/vdb-copy.dir/helper.c.o" "CMakeFiles/vdb-copy.dir/coldefs.c.o" "CMakeFiles/vdb-copy.dir/get_platform.c.o" "CMakeFiles/vdb-copy.dir/namelist_tools.c.o" "CMakeFiles/vdb-copy.dir/copy_meta.c.o" "CMakeFiles/vdb-copy.dir/type_matcher.c.o" "CMakeFiles/vdb-copy.dir/redactval.c.o" "CMakeFiles/vdb-copy.dir/config_values.c.o" "CMakeFiles/vdb-copy.dir/vdb-copy.c.o" -o ../../../bin/vdb-copy /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f meta-copy.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-correct.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv meta-copy meta-copy.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-correct pacbio-correct.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-copy.3.0.3 meta-copy.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-copy.3 meta-copy +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-correct.3.0.3 pacbio-correct.3 +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd 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/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-copy vdb-copy.3.0.3 make -f tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/build.make tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/depend -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/sortreadtest.c.o -MF CMakeFiles/sortreadtest.dir/sortreadtest.c.o.d -o CMakeFiles/sortreadtest.dir/sortreadtest.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/sortreadtest/sortreadtest.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/DependInfo.cmake --color= -[ 74%] Linking C executable ../../../bin/test-download +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-copy.3.0.3 vdb-copy.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/build.make tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-download.dir/link.txt --verbose=1 -[ 74%] Linking C executable ../../../bin/schema-replace +make -f tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/build.make tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/build +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-copy.3 vdb-copy make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cmake -E copy /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/vdb-copy.kfg /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/ncbi/vdb-copy.kfg +[ 76%] Linking C executable ../../../bin/schema-replace cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/schema-replace && /usr/bin/cmake -E cmake_link_script CMakeFiles/schema-replace.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-download.dir/test-download.c.o" -o ../../../bin/test-download /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/build.make tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/build +[ 76%] Building C object tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/sortreadtest.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/sortreadtest.c.o -MF CMakeFiles/sortreadtest.dir/sortreadtest.c.o.d -o CMakeFiles/sortreadtest.dir/sortreadtest.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/sortreadtest/sortreadtest.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/schema-replace.dir/schema-replace.c.o" -o ../../../bin/schema-replace /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -[ 74%] Building C object tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/rowwritetest.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/rowwritetest.c.o -MF CMakeFiles/rowwritetest.dir/rowwritetest.c.o.d -o CMakeFiles/rowwritetest.dir/rowwritetest.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c -[ 74%] Built target idx-text-checklookup +[ 76%] Built target vdb-copy +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/samview-util/CMakeFiles/samview-util.dir/build.make tools/test-tools/samview-util/CMakeFiles/samview-util.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/samview-util /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util/CMakeFiles/samview-util.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f cg-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv cg-load cg-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-correct.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cg-load.3.0.3 cg-load.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-correct pacbio-correct.3.0.3 +[ 76%] Building C object tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/rowwritetest.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/rowwritetest.c.o -MF CMakeFiles/rowwritetest.dir/rowwritetest.c.o.d -o CMakeFiles/rowwritetest.dir/rowwritetest.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f schema-replace.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv schema-replace schema-replace.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cg-load.3 cg-load make -f tools/test-tools/samview-util/CMakeFiles/samview-util.dir/build.make tools/test-tools/samview-util/CMakeFiles/samview-util.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-correct.3.0.3 pacbio-correct.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s schema-replace.3.0.3 schema-replace.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 76%] Linking CXX executable ../../../bin/align-cache +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache && /usr/bin/cmake -E cmake_link_script CMakeFiles/align-cache.dir/link.txt --verbose=1 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s schema-replace.3 schema-replace make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-correct.3 pacbio-correct -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 74%] Building C object tools/test-tools/samview-util/CMakeFiles/samview-util.dir/samview.c.o +[ 76%] Built target schema-replace +make -f tools/test-tools/testld/CMakeFiles/testld.dir/build.make tools/test-tools/testld/CMakeFiles/testld.dir/depend +[ 76%] Building C object tools/test-tools/samview-util/CMakeFiles/samview-util.dir/samview.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/samview-util/CMakeFiles/samview-util.dir/samview.c.o -MF CMakeFiles/samview-util.dir/samview.c.o.d -o CMakeFiles/samview-util.dir/samview.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/samview-util/samview.c -[ 74%] Built target cg-load +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/testld /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld/CMakeFiles/testld.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/align-cache.dir/align-cache.cpp.o" "CMakeFiles/align-cache.dir/helper.cpp.o" -o ../../../bin/align-cache /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +[ 76%] Linking C executable ../../../bin/test-download +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-download.dir/link.txt --verbose=1 +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/test-tools/testld/CMakeFiles/testld.dir/build.make tools/test-tools/testld/CMakeFiles/testld.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-download.dir/test-download.c.o" -o ../../../bin/test-download /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 76%] Building C object tools/test-tools/testld/CMakeFiles/testld.dir/testld.c.o /build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c: In function 'run': /build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c:287: warning: "STATUS" redefined 287 | #define STATUS(action) (action FORMAT, tablePath, name) @@ -5709,178 +5825,155 @@ /usr/include/ncbi-vdb/klib/status.h:139: note: this is the location of the previous definition 139 | #define STATUS( lvl, ... ) \ | -make -f tools/test-tools/testld/CMakeFiles/testld.dir/build.make tools/test-tools/testld/CMakeFiles/testld.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/testld /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld/CMakeFiles/testld.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f schema-replace.3.0.3 -[ 74%] Built target pacbio-correct -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv schema-replace schema-replace.3.0.3 -make -f tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build.make tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/depend -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/txt2kdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/DependInfo.cmake --color= -make -f tools/test-tools/testld/CMakeFiles/testld.dir/build.make tools/test-tools/testld/CMakeFiles/testld.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s schema-replace.3.0.3 schema-replace.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/testld/CMakeFiles/testld.dir/testld.c.o -MF CMakeFiles/testld.dir/testld.c.o.d -o CMakeFiles/testld.dir/testld.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/testld/testld.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-download.3.0.3 -[ 74%] Linking C executable ../../../bin/sortreadtest -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/sortreadtest.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s schema-replace.3 schema-replace cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv test-download test-download.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-download.3.0.3 test-download.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-download.3 test-download make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build.make tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 76%] Built target test-download +[ 76%] Linking C executable ../../../bin/samview-util +make -f tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build.make tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/depend +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util && /usr/bin/cmake -E cmake_link_script CMakeFiles/samview-util.dir/link.txt --verbose=1 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 74%] Building C object tools/test-tools/testld/CMakeFiles/testld.dir/testld.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/testld/CMakeFiles/testld.dir/testld.c.o -MF CMakeFiles/testld.dir/testld.c.o.d -o CMakeFiles/testld.dir/testld.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/testld/testld.c -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/sortreadtest.dir/sortreadtest.c.o -o ../../../bin/sortreadtest /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-download.3 test-download +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/txt2kdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/DependInfo.cmake --color= +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/samview-util.dir/samview.c.o" -o ../../../bin/samview-util /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 74%] Built target schema-replace -[ 74%] Building C object tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/txt2kdb.c.o +make -f tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build.make tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 76%] Building C object tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/txt2kdb.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/txt2kdb.c.o -MF CMakeFiles/txt2kdb.dir/txt2kdb.c.o.d -o CMakeFiles/txt2kdb.dir/txt2kdb.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/txt2kdb/txt2kdb.c +[ 76%] Linking C executable ../../../bin/testld +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld && /usr/bin/cmake -E cmake_link_script CMakeFiles/testld.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/testld.dir/testld.c.o -o ../../../bin/testld /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f samview-util.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv samview-util samview-util.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview-util.3.0.3 samview-util.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview-util.3 samview-util +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f testld.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv testld testld.3.0.3 +[ 76%] Built target samview-util +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s testld.3.0.3 testld.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s testld.3 testld +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 76%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o -MF CMakeFiles/sratools.dir/SDL-response.cpp.o.d -o CMakeFiles/sratools.dir/SDL-response.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/SDL-response.cpp +[ 76%] Built target testld make -f test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/build.make test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/DependInfo.cmake --color= -[ 74%] Linking C executable ../../../bin/samview-util -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util && /usr/bin/cmake -E cmake_link_script CMakeFiles/samview-util.dir/link.txt --verbose=1 -[ 74%] Built target test-download -make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/build.make test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/samview-util.dir/samview.c.o" -o ../../../bin/samview-util /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 74%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctar.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f align-cache.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv align-cache align-cache.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-cache.3.0.3 align-cache.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-cache.3 align-cache +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 76%] Building Java objects for test-ngs-java.jar +[ 76%] Built target align-cache +cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClearClassFiles.cmake +make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctar.c.o -MF CMakeFiles/copycat.dir/cctar.c.o.d -o CMakeFiles/copycat.dir/cctar.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build +cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/javac -classpath :/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java/junit-4.11.jar:/build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java/junit-4.11.jar -d /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir @/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/java_sources make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 74%] Building Java objects for test-ngs-java.jar +[ 76%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o -MF CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o.d -o CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-build-version.cpp +/build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c: In function 'KMain': +/build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c:383:17: warning: '__builtin_strncpy' specified bound 512 equals destination size [-Wstringop-truncation] + 383 | strncpy (tablePath, pc, sizeof (tablePath)); + | ^ +[ 76%] Linking C executable ../../../bin/sortreadtest +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/sortreadtest.dir/link.txt --verbose=1 +[ 76%] Linking C executable ../../../bin/txt2kdb +[ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o -MF CMakeFiles/sratools.dir/tool-args.cpp.o.d -o CMakeFiles/sratools.dir/tool-args.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/tool-args.cpp +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb && /usr/bin/cmake -E cmake_link_script CMakeFiles/txt2kdb.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/sortreadtest.dir/sortreadtest.c.o -o ../../../bin/sortreadtest /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +[ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o -MF CMakeFiles/sratools.dir/build-version.cpp.o.d -o CMakeFiles/sratools.dir/build-version.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/build-version.cpp +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/txt2kdb.dir/txt2kdb.c.o -o ../../../bin/txt2kdb /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +[ 77%] Linking C executable ../../../bin/rowwritetest +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest && /usr/bin/cmake -E cmake_link_script CMakeFiles/rowwritetest.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/rowwritetest.dir/rowwritetest.c.o -o ../../../bin/rowwritetest /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sortreadtest.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClearClassFiles.cmake cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sortreadtest sortreadtest.3.0.3 -[ 74%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o -MF CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o.d -o CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-build-version.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sortreadtest.3.0.3 sortreadtest.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sortreadtest.3 sortreadtest -cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/javac -classpath :/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java/junit-4.11.jar:/build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java/junit-4.11.jar -d /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir @/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/java_sources make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 74%] Built target sortreadtest +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f txt2kdb.3.0.3 +[ 77%] Built target sortreadtest make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/depend +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv txt2kdb txt2kdb.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s txt2kdb.3.0.3 txt2kdb.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s txt2kdb.3 txt2kdb +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/DependInfo.cmake --color= -/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c: In function 'what_header_type': -/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c:1015:42: warning: the comparison will always evaluate as 'true' for the address of 'fullsize' will never be NULL [-Waddress] - 1015 | header->suntar.extcount && - | ^~ -/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c:598:25: note: 'fullsize' declared here - 598 | sun_fullsize fullsize; /* 502 non-conformant */ - | ^~~~~~~~ -[ 75%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/redactval.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/redactval.c.o -MF CMakeFiles/vdb-copy.dir/redactval.c.o.d -o CMakeFiles/vdb-copy.dir/redactval.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/redactval.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f samview-util.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv samview-util samview-util.3.0.3 -[ 75%] Linking C executable ../../../bin/testld +[ 77%] Built target txt2kdb +make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/depend make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld && /usr/bin/cmake -E cmake_link_script CMakeFiles/testld.dir/link.txt --verbose=1 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview-util.3.0.3 samview-util.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview-util.3 samview-util -[ 75%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o -MF CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o.d -o CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-filepath.cpp -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/testld.dir/testld.c.o -o ../../../bin/testld /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 75%] Built target samview-util -make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/DependInfo.cmake --color= -[ 75%] Linking CXX executable ../../../../test-bin/makeinputs +[ 77%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o -MF CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o.d -o CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-filepath.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/makeinputs.dir/link.txt --verbose=1 +[ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o -MF CMakeFiles/sratools.dir/file-path.posix.cpp.o.d -o CMakeFiles/sratools.dir/file-path.posix.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/file-path.posix.cpp make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c: In function 'KMain': -/build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c:383:17: warning: '__builtin_strncpy' specified bound 512 equals destination size [-Wstringop-truncation] - 383 | strncpy (tablePath, pc, sizeof (tablePath)); - | ^ -[ 75%] Linking C executable ../../../bin/txt2kdb -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb && /usr/bin/cmake -E cmake_link_script CMakeFiles/txt2kdb.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/makeinputs.dir/makeinputs.cpp.o CMakeFiles/makeinputs.dir/testsource.cpp.o -o ../../../../test-bin/makeinputs ../../../../ilib/libgeneral-writer.a -lncbi-vdb -[ 75%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o +[ 77%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o -MF CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o.d -o CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-command-line.cpp -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/txt2kdb.dir/txt2kdb.c.o -o ../../../bin/txt2kdb /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f testld.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv testld testld.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s testld.3.0.3 testld.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s testld.3 testld +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f rowwritetest.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv rowwritetest rowwritetest.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rowwritetest.3.0.3 rowwritetest.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rowwritetest.3 rowwritetest make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 75%] Linking C executable ../../../bin/rowwritetest -[ 75%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/config_values.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest && /usr/bin/cmake -E cmake_link_script CMakeFiles/rowwritetest.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/config_values.c.o -MF CMakeFiles/vdb-copy.dir/config_values.c.o.d -o CMakeFiles/vdb-copy.dir/config_values.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/config_values.c -[ 75%] Built target testld -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/rowwritetest.dir/rowwritetest.c.o -o ../../../bin/rowwritetest /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +[ 77%] Built target rowwritetest make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f txt2kdb.3.0.3 -[ 75%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/main.cpp.o -[ 76%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccsra.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv txt2kdb txt2kdb.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccsra.c.o -MF CMakeFiles/copycat.dir/ccsra.c.o.d -o CMakeFiles/copycat.dir/ccsra.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccsra.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/main.cpp.o -MF CMakeFiles/general-loader.dir/main.cpp.o.d -o CMakeFiles/general-loader.dir/main.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/main.cpp make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s txt2kdb.3.0.3 txt2kdb.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s txt2kdb.3 txt2kdb -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 76%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o +[ 77%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o -MF CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o.d -o CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-json-parse.cpp -[ 76%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/vdb-copy.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/vdb-copy.c.o -MF CMakeFiles/vdb-copy.dir/vdb-copy.c.o.d -o CMakeFiles/vdb-copy.dir/vdb-copy.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/vdb-copy.c -[ 76%] Built target txt2kdb +[ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o -MF CMakeFiles/sratools.dir/proc.posix.cpp.o.d -o CMakeFiles/sratools.dir/proc.posix.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp +[ 77%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/main.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/main.cpp.o -MF CMakeFiles/general-loader.dir/main.cpp.o.d -o CMakeFiles/general-loader.dir/main.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/main.cpp +[ 77%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/testsource.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/testsource.cpp.o -MF CMakeFiles/test-general-loader.dir/testsource.cpp.o.d -o CMakeFiles/test-general-loader.dir/testsource.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp +/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp: In member function 'POSIX::Process::ExitStatus POSIX::Process::wait() const': +/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp:246:28: warning: 'void std::unexpected()' is deprecated [-Wdeprecated-declarations] + 246 | std::unexpected(); + | ~~~~~~~~~~~~~~~^~ +In file included from /usr/include/c++/12/ios:39, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp:42: +/usr/include/c++/12/exception:109:8: note: declared here + 109 | void unexpected() __attribute__ ((__noreturn__)); + | ^~~~~~~~~~ +[ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_BuildVersion +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_BuildVersion.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o" -o ../../../test-bin/Test_Drivertool_BuildVersion +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 77%] Built target Test_Drivertool_BuildVersion make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f rowwritetest.3.0.3 -[ 76%] Built target makeinputs -make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/depend -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv rowwritetest rowwritetest.3.0.3 -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rowwritetest.3.0.3 rowwritetest.3 -[ 76%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rowwritetest.3 rowwritetest +[ 77%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o -MF CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o.d -o CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-sdl-response.cpp -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 76%] Built target rowwritetest -make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/depend -[ 77%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o -MF CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o.d -o CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-accession.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool 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tools/internal/copycat/CMakeFiles/copycat.dir/ccfile.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccfile.c.o -MF CMakeFiles/copycat.dir/ccfile.c.o.d -o CMakeFiles/copycat.dir/ccfile.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccfile.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:2340:41: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 2340 | if (!isPrimary && AR_MAPQ(data) < G.minMapQual) -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f align-cache.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv align-cache align-cache.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-cache.3.0.3 align-cache.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-cache.3 align-cache +[ 77%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/mem-bank.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/mem-bank.cpp.o -MF CMakeFiles/bam-load.dir/mem-bank.cpp.o.d -o CMakeFiles/bam-load.dir/mem-bank.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/mem-bank.cpp +make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target align-cache -[ 77%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/fileformat.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/fileformat.c.o -MF CMakeFiles/copycat.dir/kff/fileformat.c.o.d -o CMakeFiles/copycat.dir/kff/fileformat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/fileformat.c -[ 77%] Linking C executable ../../../bin/vdb-copy -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-copy.dir/link.txt --verbose=1 -[ 77%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffext.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffext.c.o -MF CMakeFiles/copycat.dir/kff/ffext.c.o.d -o CMakeFiles/copycat.dir/kff/ffext.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffext.c -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-copy.dir/context.c.o" "CMakeFiles/vdb-copy.dir/helper.c.o" "CMakeFiles/vdb-copy.dir/coldefs.c.o" "CMakeFiles/vdb-copy.dir/get_platform.c.o" "CMakeFiles/vdb-copy.dir/namelist_tools.c.o" "CMakeFiles/vdb-copy.dir/copy_meta.c.o" "CMakeFiles/vdb-copy.dir/type_matcher.c.o" "CMakeFiles/vdb-copy.dir/redactval.c.o" "CMakeFiles/vdb-copy.dir/config_values.c.o" "CMakeFiles/vdb-copy.dir/vdb-copy.c.o" -o ../../../bin/vdb-copy /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-copy.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-copy vdb-copy.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-copy.3.0.3 vdb-copy.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-copy.3 vdb-copy -[ 77%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffkey.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cmake -E copy /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/vdb-copy.kfg /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/ncbi/vdb-copy.kfg -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffkey.c.o -MF CMakeFiles/copycat.dir/kff/ffkey.c.o.d -o CMakeFiles/copycat.dir/kff/ffkey.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffkey.c -[ 77%] Linking CXX executable ../../../bin/general-loader +make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 78%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o -MF CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o.d -o CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-accession.cpp +[ 78%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/low-match-count.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/low-match-count.cpp.o -MF CMakeFiles/bam-load.dir/low-match-count.cpp.o.d -o CMakeFiles/bam-load.dir/low-match-count.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/low-match-count.cpp +[ 78%] Linking CXX executable ../../../bin/general-loader cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/general-loader.dir/link.txt --verbose=1 -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/general-loader.dir/general-loader.cpp.o" "CMakeFiles/general-loader.dir/protocol-parser.cpp.o" "CMakeFiles/general-loader.dir/database-loader.cpp.o" "CMakeFiles/general-loader.dir/main.cpp.o" -o ../../../bin/general-loader ../../../ilib/libgeneral-writer.a ../../../ilib/libloader.a -lkapp ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -[ 77%] Built target vdb-copy +Note: ngs_test_lib_load.java uses unchecked or unsafe operations. +Note: Recompile with -Xlint:unchecked for details. +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f general-loader.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv general-loader general-loader.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s general-loader.3.0.3 general-loader.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s general-loader.3 general-loader +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 78%] Built target general-loader +make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/build +cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -E touch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/java_compiled_test-ngs-java +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 78%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o -MF CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o.d -o CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-uuid.cpp +[ 78%] Generating CMakeFiles/test-ngs-java.dir/java_class_filelist +cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClassFilelist.cmake +[ 78%] Creating Java archive test-ngs-java.jar +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir && /usr/bin/jar -cf /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/test-ngs-java.jar @java_class_filelist +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=test-ngs-java.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.25/Modules/UseJava/Symlinks.cmake +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 78%] Built target test-ngs-java make -f test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/build.make test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/vdb-config /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/build.make test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffmagic.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffmagic.c.o -MF CMakeFiles/copycat.dir/kff/ffmagic.c.o.d -o CMakeFiles/copycat.dir/kff/ffmagic.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffmagic.c -[ 77%] Building CXX object test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o +[ 78%] Building CXX object test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o -MF CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o.d -o CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/vdb-config/test-vdb-config-model.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f general-loader.3.0.3 -[ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_BuildVersion -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_BuildVersion.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv general-loader general-loader.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s general-loader.3.0.3 general-loader.3 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o" -o ../../../test-bin/Test_Drivertool_BuildVersion -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s general-loader.3 general-loader +[ 78%] Linking CXX executable ../../../test-bin/Test_Drivertool_CommandLine +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_CommandLine.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o" -o ../../../test-bin/Test_Drivertool_CommandLine make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target general-loader +[ 78%] Built target Test_Drivertool_CommandLine make -f test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/build.make test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/DependInfo.cmake --color= -[ 77%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/mem-bank.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/mem-bank.cpp.o -MF CMakeFiles/bam-load.dir/mem-bank.cpp.o.d -o CMakeFiles/bam-load.dir/mem-bank.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/mem-bank.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/build.make test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Building CXX object test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o +[ 78%] Building CXX object test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o -MF CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o.d -o CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/vdb-dump/makedb.cpp -[ 77%] Linking C executable ../../../bin/copycat -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cmake -E cmake_link_script CMakeFiles/copycat.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/copycat.dir/copycat.c.o CMakeFiles/copycat.dir/ccfileformat.c.o CMakeFiles/copycat.dir/cccat.c.o CMakeFiles/copycat.dir/cctree.c.o "CMakeFiles/copycat.dir/cctree-dump.c.o" CMakeFiles/copycat.dir/cctar.c.o CMakeFiles/copycat.dir/ccsra.c.o CMakeFiles/copycat.dir/ccsubchunk.c.o CMakeFiles/copycat.dir/ccfile.c.o CMakeFiles/copycat.dir/kff/fileformat.c.o CMakeFiles/copycat.dir/kff/ffext.c.o CMakeFiles/copycat.dir/kff/ffkey.c.o CMakeFiles/copycat.dir/kff/ffmagic.c.o -o ../../../bin/copycat /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libmagic.so -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target Test_Drivertool_BuildVersion make -f test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/build.make test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/build.make test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Building C object test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o +[ 78%] Building C object test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/loaders/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o -MF CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o.d -o CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o -c /build/sra-sdk-3.0.3+dfsg/test/loaders/loader/qfiletest.c -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f copycat.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv copycat copycat.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s copycat.3.0.3 copycat.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s copycat.3 copycat -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target copycat make -f test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -Note: ngs_test_lib_load.java uses unchecked or unsafe operations. -Note: Recompile with -Xlint:unchecked for details. -[ 77%] Building CXX object test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o +[ 78%] Building CXX object test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/loaders/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o -MF CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o.d -o CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/loaders/loader/test-loaderfile.cpp -[ 77%] Linking C executable ../../../test-bin/Test_KAPP_qfile +[ 78%] Linking C executable ../../../test-bin/Test_KAPP_qfile cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_KAPP_qfile.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o -o ../../../test-bin/Test_KAPP_qfile ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -E touch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/java_compiled_test-ngs-java -[ 77%] Generating CMakeFiles/test-ngs-java.dir/java_class_filelist -cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClassFilelist.cmake -[ 77%] Creating Java archive test-ngs-java.jar -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir && /usr/bin/jar -cf /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/test-ngs-java.jar @java_class_filelist -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target Test_KAPP_qfile +/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c: In function 'sqlite3SelectNew': +/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:115649:10: warning: function may return address of local variable [-Wreturn-local-addr] +115649 | return pNew; + | ^~~~ make -f test/loaders/loader/CMakeFiles/Test_LOADER.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADER.dir/depend +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_LOADER.dir/DependInfo.cmake --color= +/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:115609:10: note: declared here +115609 | Select standin; + | ^~~~~~~ +[ 78%] Built target Test_KAPP_qfile +make -f test/loaders/sharq/CMakeFiles/test-regexpr.dir/build.make test/loaders/sharq/CMakeFiles/test-regexpr.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq/CMakeFiles/test-regexpr.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/loader/CMakeFiles/Test_LOADER.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADER.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_UUID -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_UUID.dir/link.txt --verbose=1 -[ 77%] Building CXX object test/loaders/loader/CMakeFiles/Test_LOADER.dir/loadertest.cpp.o +[ 78%] Building CXX object test/loaders/loader/CMakeFiles/Test_LOADER.dir/loadertest.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/loaders/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/loaders/loader/CMakeFiles/Test_LOADER.dir/loadertest.cpp.o -MF CMakeFiles/Test_LOADER.dir/loadertest.cpp.o.d -o CMakeFiles/Test_LOADER.dir/loadertest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/loaders/loader/loadertest.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o" -o ../../../test-bin/Test_Drivertool_UUID -[ 77%] Linking CXX executable ../../../test-bin/vdb-dump-makedb -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-dump-makedb.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o" -o ../../../test-bin/vdb-dump-makedb /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f test/loaders/sharq/CMakeFiles/test-regexpr.dir/build.make test/loaders/sharq/CMakeFiles/test-regexpr.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 78%] Building CXX object test/loaders/sharq/CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT test/loaders/sharq/CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o -MF CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o.d -o CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp /build/sra-sdk-3.0.3+dfsg/test/loaders/loader/loadertest.cpp:307:117: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 307 | REQUIRE_RC ( KLoaderMeta_Write ( node, LoaderName.c_str(), __DATE__, FormatterName.c_str(), KAppVersion() ) ); | ^ @@ -6015,49 +6103,42 @@ /build/sra-sdk-3.0.3+dfsg/test/loaders/loader/loadertest.cpp:364:80: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 364 | REQUIRE_EQ ( string ( __DATE__), GetMetadata ( "SOFTWARE/loader", "date" ) ); | ^ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=test-ngs-java.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.25/Modules/UseJava/Symlinks.cmake -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target Test_Drivertool_UUID -make -f test/loaders/sharq/CMakeFiles/test-regexpr.dir/build.make test/loaders/sharq/CMakeFiles/test-regexpr.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq/CMakeFiles/test-regexpr.dir/DependInfo.cmake --color= -[ 77%] Built target test-ngs-java make -f test/internal/align/CMakeFiles/Test_Align_samextract.dir/build.make test/internal/align/CMakeFiles/Test_Align_samextract.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/internal/align /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align/CMakeFiles/Test_Align_samextract.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f test/loaders/sharq/CMakeFiles/test-regexpr.dir/build.make test/loaders/sharq/CMakeFiles/test-regexpr.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/internal/align/CMakeFiles/Test_Align_samextract.dir/build.make test/internal/align/CMakeFiles/Test_Align_samextract.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Building CXX object test/loaders/sharq/CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT test/loaders/sharq/CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o -MF CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o.d -o CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp -[ 77%] Building CXX object test/internal/align/CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o +[ 78%] Building CXX object test/internal/align/CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/align\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/ext -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/../ncbi-vdb/interfaces/ext -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/internal/align/CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o -MF CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o.d -o CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/internal/align/test-samextract.cpp +[ 78%] Linking CXX executable ../../../test-bin/Test_Drivertool_UUID +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_UUID.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o" -o ../../../test-bin/Test_Drivertool_UUID make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_Accession -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_Accession.dir/link.txt --verbose=1 -[ 77%] Built target vdb-dump-makedb -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o" -o ../../../test-bin/Test_Drivertool_Accession -[ 77%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/low-match-count.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/low-match-count.cpp.o -MF CMakeFiles/bam-load.dir/low-match-count.cpp.o.d -o CMakeFiles/bam-load.dir/low-match-count.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/low-match-count.cpp -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target Test_Drivertool_Accession +[ 78%] Built target Test_Drivertool_UUID make -f ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build.make ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/depend -[ 77%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/testsource.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-c++ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/testsource.cpp.o -MF CMakeFiles/test-general-loader.dir/testsource.cpp.o.d -o CMakeFiles/test-general-loader.dir/testsource.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build.make ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build +[ 78%] Linking CXX executable ../../../test-bin/Test_Drivertool_Accession +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_Accession.dir/link.txt --verbose=1 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Building CXX object ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o +[ 78%] Building CXX object ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-c++\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o -MF CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o.d -o CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-c++/NCBI-NGS.cpp -[ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_CommandLine -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_CommandLine.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o" -o ../../../test-bin/Test_Drivertool_CommandLine +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o" -o ../../../test-bin/Test_Drivertool_Accession +[ 78%] Linking CXX executable ../../../test-bin/vdb-dump-makedb +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-dump-makedb.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o" -o ../../../test-bin/vdb-dump-makedb /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 78%] Built target Test_Drivertool_Accession +make -f ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc && bash -c /usr/bin/jar\ -cf\ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-doc.jar\ . In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6074,28 +6155,7 @@ 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target Test_Drivertool_CommandLine -make -f ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc && bash -c /usr/bin/jar\ -cf\ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-doc.jar\ . -[ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/proc.cpp.o -MF CMakeFiles/sratools.dir/proc.cpp.o.d -o CMakeFiles/sratools.dir/proc.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.cpp -[ 77%] Linking CXX static library ../../../lib/libncbi-ngs-c++.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/cmake -P CMakeFiles/ncbi-ngs-c++.dir/cmake_clean_target.cmake -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs-c++.dir/link.txt --verbose=1 -/usr/bin/ar qc ../../../lib/libncbi-ngs-c++.a "CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" -/usr/bin/ranlib ../../../lib/libncbi-ngs-c++.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && rm -f libncbi-ngs-c++.a.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && mv libncbi-ngs-c++.a libncbi-ngs-c++.a.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a.3.0.3 libncbi-ngs-c++.a.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a.3 libncbi-ngs-c++.a -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a libncbi-ngs-c++-static.a -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target ncbi-ngs-c++ +[ 78%] Built target vdb-dump-makedb make -f ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/DependInfo.cmake --color= @@ -6104,37 +6164,37 @@ make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && bash -c /usr/bin/jar\ -cf\ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-src.jar\ \ ngs/ErrorMsg.java\ ngs/Statistics.java\ ngs/Fragment.java\ ngs/FragmentIterator.java\ ngs/Read.java\ ngs/ReadIterator.java\ ngs/ReadGroup.java\ ngs/ReadGroupIterator.java\ ngs/Alignment.java\ ngs/AlignmentIterator.java\ ngs/PileupEvent.java\ ngs/PileupEventIterator.java\ ngs/Pileup.java\ ngs/PileupIterator.java\ ngs/Reference.java\ ngs/ReferenceIterator.java\ ngs/ReadCollection.java\ ngs/Package.java\ ngs/itf/Refcount.java\ ngs/itf/StatisticsItf.java\ ngs/itf/FragmentItf.java\ ngs/itf/FragmentIteratorItf.java\ ngs/itf/ReadItf.java\ ngs/itf/ReadIteratorItf.java\ ngs/itf/ReadGroupItf.java\ ngs/itf/ReadGroupIteratorItf.java\ ngs/itf/AlignmentItf.java\ ngs/itf/AlignmentIteratorItf.java\ ngs/itf/PileupEventItf.java\ ngs/itf/PileupEventIteratorItf.java\ ngs/itf/PileupItf.java\ ngs/itf/PileupIteratorItf.java\ ngs/itf/ReferenceItf.java\ ngs/itf/ReferenceIteratorItf.java\ ngs/itf/ReadCollectionItf.java\ gov/nih/nlm/ncbi/ngs/DownloadManager.java\ gov/nih/nlm/ncbi/ngs/FileCreator.java\ gov/nih/nlm/ncbi/ngs/HttpManager.java\ gov/nih/nlm/ncbi/ngs/LibDependencies.java\ gov/nih/nlm/ncbi/ngs/LibManager.java\ gov/nih/nlm/ncbi/ngs/LibPathIterator.java\ gov/nih/nlm/ncbi/ngs/LibVersionChecker.java\ gov/nih/nlm/ncbi/ngs/LMProperties.java\ gov/nih/nlm/ncbi/ngs/Logger.java\ gov/nih/nlm/ncbi/ngs/Manager.java\ gov/nih/nlm/ncbi/ngs/NGS.java\ gov/nih/nlm/ncbi/ngs/Version.java\ gov/nih/nlm/ncbi/ngs/error/LibraryLoadError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryNotFoundError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryIncompatibleVersionError.java\ gov/nih/nlm/ncbi/ngs/error/cause/ConnectionProblemCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/DownloadDisabledCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/InvalidLibraryCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/JvmErrorCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/LibraryLoadCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/OutdatedJarCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/PrereleaseReqLibCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target ngs-doc-jar +[ 78%] Built target ngs-src-jar make -f ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/build.make ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 78%] Built target ngs-doc-jar +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/build.make ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Building Java objects for ngs-examples.jar -cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClearClassFiles.cmake -cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/javac -classpath :/build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar -d /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir @/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_sources make -f libs/general-writer/CMakeFiles/gw-dumper.dir/build.make libs/general-writer/CMakeFiles/gw-dumper.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/general-writer /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/CMakeFiles/gw-dumper.dir/DependInfo.cmake --color= +[ 78%] Building Java objects for ngs-examples.jar make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/general-writer/CMakeFiles/gw-dumper.dir/build.make libs/general-writer/CMakeFiles/gw-dumper.dir/build +cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClearClassFiles.cmake make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Building CXX object libs/general-writer/CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o +[ 78%] Building CXX object libs/general-writer/CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/general-writer/CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o -MF CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o.d -o CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp +cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/javac -classpath :/build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar -d /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir @/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_sources +[ 78%] Linking CXX static library ../../../lib/libncbi-ngs-c++.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/cmake -P CMakeFiles/ncbi-ngs-c++.dir/cmake_clean_target.cmake +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs-c++.dir/link.txt --verbose=1 +/usr/bin/ar qc ../../../lib/libncbi-ngs-c++.a "CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" +/usr/bin/ranlib ../../../lib/libncbi-ngs-c++.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && rm -f libncbi-ngs-c++.a.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && mv libncbi-ngs-c++.a libncbi-ngs-c++.a.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a.3.0.3 libncbi-ngs-c++.a.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a.3 libncbi-ngs-c++.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a libncbi-ngs-c++-static.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target ngs-src-jar -make -f libs/general-writer/test/CMakeFiles/test-general-writer.dir/build.make libs/general-writer/test/CMakeFiles/test-general-writer.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/general-writer/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test/CMakeFiles/test-general-writer.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/general-writer/test/CMakeFiles/test-general-writer.dir/build.make libs/general-writer/test/CMakeFiles/test-general-writer.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Building CXX object libs/general-writer/test/CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/general-writer/test/CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o -MF CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o.d -o CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp -[ 77%] Linking CXX executable ../../../test-bin/Test_LOADERFILE -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_LOADERFILE.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o" -o ../../../test-bin/Test_LOADERFILE ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp: In member function 'void Construction::Instance::test_method()': /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp:40:22: warning: parentheses were disambiguated as a function declaration [-Wvexing-parse] 40 | CRegExprMatcher m( string() ); @@ -6145,33 +6205,25 @@ | - | { - | } -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target Test_LOADERFILE -make -f tools/external/prefetch/CMakeFiles/prefetch.dir/build.make tools/external/prefetch/CMakeFiles/prefetch.dir/depend +[ 78%] Built target ncbi-ngs-c++ +make -f libs/general-writer/test/CMakeFiles/test-general-writer.dir/build.make libs/general-writer/test/CMakeFiles/test-general-writer.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/prefetch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch/CMakeFiles/prefetch.dir/DependInfo.cmake --color= +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/general-writer/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test/CMakeFiles/test-general-writer.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/prefetch/CMakeFiles/prefetch.dir/build.make tools/external/prefetch/CMakeFiles/prefetch.dir/build +make -f libs/general-writer/test/CMakeFiles/test-general-writer.dir/build.make libs/general-writer/test/CMakeFiles/test-general-writer.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c: In function 'sqlite3SelectNew': -[ 77%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/kfile-no-q.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/kfile-no-q.c.o -MF CMakeFiles/prefetch.dir/kfile-no-q.c.o.d -o CMakeFiles/prefetch.dir/kfile-no-q.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/prefetch/kfile-no-q.c -/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:115649:10: warning: function may return address of local variable [-Wreturn-local-addr] -115649 | return pNew; - | ^~~~ +[ 78%] Building CXX object libs/general-writer/test/CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/general-writer/test/CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o -MF CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o.d -o CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp: In function 'void gw_dump::check_vers_component(const char*, const char*, long int, long unsigned int, char)': /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:1198:29: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare] 1198 | if ( num < 0 || num > max ) | ~~~~^~~~~ -/build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:115609:10: note: declared here -115609 | Select standin; - | ^~~~~~~ -[ 78%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfMain.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/PrfMain.c.o -MF CMakeFiles/prefetch.dir/PrfMain.c.o.d -o CMakeFiles/prefetch.dir/PrfMain.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/prefetch/PrfMain.c /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp: In function 'const char* gw_dump::metadata_node_root_name(metadata_node_root)': /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:1315:5: warning: control reaches end of non-void function [-Wreturn-type] 1315 | } | ^ +cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -E touch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_compiled_ngs-examples +[ 78%] Generating CMakeFiles/ngs-examples.dir/java_class_filelist /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp: At global scope: /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:732:17: warning: 'char gw_dump::hex(uint8_t)' defined but not used [-Wunused-function] 732 | static char hex(uint8_t const x) { @@ -6182,6 +6234,7 @@ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:418:12: warning: 'char* gw_dump::read_colname(const T&, FILE*) [with T = gw_column_evt_v1]' defined but not used [-Wunused-function] 418 | char * read_colname < :: gw_column_evt_v1 > ( const :: gw_column_evt_v1 & eh, FILE * in ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClassFilelist.cmake /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:368:10: warning: 'void gw_dump::whack_2string(const T&, char*) [with T = gw_2string_evt_v1]' defined but not used [-Wunused-function] 368 | void whack_2string < :: gw_2string_evt_v1 > ( const :: gw_2string_evt_v1 & eh, char * string_buffer ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6197,68 +6250,58 @@ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:255:12: warning: 'char* gw_dump::read_1string(const T&, FILE*) [with T = gw_1string_evt_v1]' defined but not used [-Wunused-function] 255 | char * read_1string < :: gw_1string_evt_v1 > ( const :: gw_1string_evt_v1 & eh, FILE * in ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 78%] Creating Java archive ngs-examples.jar +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/bin/jar -cf /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-examples.jar @java_class_filelist +[ 79%] Linking CXX executable ../../../test-bin/Test_Drivertool_JsonParsing +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_JsonParsing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o" -o ../../../test-bin/Test_Drivertool_JsonParsing +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=ngs-examples.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.25/Modules/UseJava/Symlinks.cmake +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 79%] Built target Test_Drivertool_JsonParsing +make -f tools/external/prefetch/CMakeFiles/prefetch.dir/build.make tools/external/prefetch/CMakeFiles/prefetch.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/prefetch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch 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Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-config/CMakeFiles/vdb-config.dir/build.make tools/external/vdb-config/CMakeFiles/vdb-config.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 78%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/configure.cpp.o +[ 79%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/configure.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc 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-ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/uuid.cpp.o -MF CMakeFiles/sratools.dir/uuid.cpp.o.d -o CMakeFiles/sratools.dir/uuid.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/uuid.cpp -[ 78%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/prefetch.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/prefetch.c.o -MF CMakeFiles/prefetch.dir/prefetch.c.o.d -o CMakeFiles/prefetch.dir/prefetch.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/prefetch/prefetch.c -/build/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp: In function 'void ncbi::runTest(int, const char**, const char*, const char*)': -/build/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp:271:20: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] - 271 | delete gw; - | ^~ -/build/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp:217:24: note: 'gw' was declared here - 217 | GeneralWriter *gw; - | ^~ -cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -E touch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_compiled_ngs-examples -[ 78%] Generating CMakeFiles/ngs-examples.dir/java_class_filelist -cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClassFilelist.cmake -[ 78%] Creating Java archive ngs-examples.jar -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/bin/jar -cf /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-examples.jar @java_class_filelist -[ 79%] Linking CXX executable ../../../test-bin/test-general-writer -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-general-writer.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/bin/cmake 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-I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/kfile-no-q.c.o -MF CMakeFiles/prefetch.dir/kfile-no-q.c.o.d -o CMakeFiles/prefetch.dir/kfile-no-q.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/prefetch/kfile-no-q.c +[ 79%] Linking CXX executable ../../../test-bin/Test_LOADERFILE +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_LOADERFILE.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o" -o ../../../test-bin/Test_LOADERFILE ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 80%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfMain.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT 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-I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/spot-assembler.c.o -MF CMakeFiles/latf-load.dir/spot-assembler.c.o.d -o CMakeFiles/latf-load.dir/spot-assembler.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/spot-assembler.c -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/Test_LOADER.dir/loadertest.cpp.o -o ../../../test-bin/Test_LOADER ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 81%] Built target test-general-writer -make -f tools/loaders/sharq/CMakeFiles/sharq.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq/CMakeFiles/sharq.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/loaders/sharq/CMakeFiles/sharq.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 81%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/accession.cpp.o -[ 81%] Building CXX object tools/loaders/sharq/CMakeFiles/sharq.dir/fastq_parse.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/accession.cpp.o -MF CMakeFiles/sratools.dir/accession.cpp.o.d -o CMakeFiles/sratools.dir/accession.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/accession.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/. -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/../../.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT tools/loaders/sharq/CMakeFiles/sharq.dir/fastq_parse.cpp.o -MF CMakeFiles/sharq.dir/fastq_parse.cpp.o.d -o CMakeFiles/sharq.dir/fastq_parse.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parse.cpp -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 81%] Built target Test_LOADER -[ 81%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o -MF CMakeFiles/sratools.dir/service.cpp.o.d -o CMakeFiles/sratools.dir/service.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/service.cpp +/build/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp: In function 'void ncbi::runTest(int, const char**, const char*, const char*)': +/build/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp:271:20: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] + 271 | delete gw; + | ^~ +/build/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp:217:24: note: 'gw' was declared here + 217 | GeneralWriter *gw; + | ^~ [ 81%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-writer.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-writer.c.o -MF CMakeFiles/latf-load.dir/common-writer.c.o.d -o CMakeFiles/latf-load.dir/common-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c -[ 82%] Linking CXX executable ../../../test-bin/Test_Drivertool_JsonParsing -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_JsonParsing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o" -o ../../../test-bin/Test_Drivertool_JsonParsing +[ 81%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/prefetch.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/prefetch.c.o -MF CMakeFiles/prefetch.dir/prefetch.c.o.d -o CMakeFiles/prefetch.dir/prefetch.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/prefetch/prefetch.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c: In function 'readThread': /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:691:16: warning: pointer 'rslt' may be used after 'free' [-Wuse-after-free] 691 | if ( rr->type == rr_fileDone ) @@ -6272,90 +6315,134 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:647:13: note: call to 'free' here 647 | free(rr); | ^~~~~~~~ +[ 82%] Linking CXX executable ../../../test-bin/test-general-writer +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-general-writer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o" -o ../../../test-bin/test-general-writer ../../../ilib/libgeneral-writer.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 83%] Linking CXX executable ../../../test-bin/Test_LOADER +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_LOADER.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/Test_LOADER.dir/loadertest.cpp.o -o ../../../test-bin/Test_LOADER ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 82%] Built target Test_Drivertool_JsonParsing +[ 83%] Built target test-general-writer +make -f tools/loaders/sharq/CMakeFiles/sharq.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq/CMakeFiles/sharq.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/loaders/sharq/CMakeFiles/sharq.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.dir/build +[ 83%] Linking CXX executable ../../../test-bin/test-regexpr +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-regexpr.dir/link.txt --verbose=1 +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o" -o ../../../test-bin/test-regexpr /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -lre2 +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 83%] Building CXX object tools/loaders/sharq/CMakeFiles/sharq.dir/fastq_parse.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/. -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/../../.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT tools/loaders/sharq/CMakeFiles/sharq.dir/fastq_parse.cpp.o -MF CMakeFiles/sharq.dir/fastq_parse.cpp.o.d -o CMakeFiles/sharq.dir/fastq_parse.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parse.cpp +[ 83%] Built target Test_LOADER make -f ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 83%] Linking CXX static library ../../lib/libngs-c++.a +[ 84%] Linking CXX static library ../../lib/libngs-c++.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -P CMakeFiles/ngs-c++.dir/cmake_clean_target.cmake cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-c++.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libngs-c++.a 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"language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" 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../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 84%] Built target test-regexpr +make -f ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/depend /usr/bin/ranlib ../../lib/libngs-c++.a +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && rm -f libngs-c++.a.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && mv libngs-c++.a libngs-c++.a.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a.3.0.3 libngs-c++.a.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a.3 libngs-c++.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a libngs-c++-static.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 83%] Built target ngs-c++ -make -f ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk 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../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" -[ 83%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/sequence-writer.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/sequence-writer.c.o -MF CMakeFiles/latf-load.dir/sequence-writer.c.o.d -o CMakeFiles/latf-load.dir/sequence-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/sequence-writer.c -[ 83%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/json-parse.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/json-parse.cpp.o -MF CMakeFiles/sratools.dir/json-parse.cpp.o.d -o CMakeFiles/sratools.dir/json-parse.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/json-parse.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_symlink_library ../../lib/libngs-c++.so.3.0.3 ../../lib/libngs-c++.so.3 ../../lib/libngs-c++.so -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 83%] Built target test-regexpr +[ 84%] Built target ngs-c++ make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 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../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 83%] Built target ngs-c++-shared -make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/depend -[ 84%] Linking CXX static library ../../lib/libncbi-ngs.a +[ 85%] Linking CXX static library ../../lib/libncbi-ngs.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -P CMakeFiles/ncbi-ngs.dir/cmake_clean_target.cmake -make[3]: Entering directory 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cmake_link_script CMakeFiles/ncbi-ngs-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libncbi-ngs.a "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" 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../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" 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-D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/sequence-writer.c.o -MF CMakeFiles/latf-load.dir/sequence-writer.c.o.d -o CMakeFiles/latf-load.dir/sequence-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/sequence-writer.c /usr/bin/ranlib ../../lib/libncbi-ngs.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_symlink_library ../../lib/libngs-c++.so.3.0.3 ../../lib/libngs-c++.so.3 ../../lib/libngs-c++.so cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && rm -f libncbi-ngs.a.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && mv libncbi-ngs.a libncbi-ngs.a.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a.3.0.3 libncbi-ngs.a.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a.3 libncbi-ngs.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a libncbi-ngs-static.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 84%] Built target ncbi-ngs +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 85%] Built target ngs-c++-shared +make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/DependInfo.cmake --color= +[ 85%] Built target ncbi-ngs +[ 85%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-reader.c.o +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-reader.c.o -MF CMakeFiles/latf-load.dir/common-reader.c.o.d -o CMakeFiles/latf-load.dir/common-reader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-reader.c +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 85%] Linking CXX shared library ../../lib/libncbi-ngs.so +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs-shared.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libncbi-ngs.so.3 -o 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../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" 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"../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" /usr/lib/x86_64-linux-gnu/libkapp.a ../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 85%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-reader.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-reader.c.o -MF CMakeFiles/latf-load.dir/fastq-reader.c.o.d -o CMakeFiles/latf-load.dir/fastq-reader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-reader.c +[ 85%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o -MF CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o.d -o CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-grammar.c +[ 85%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-lex.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-lex.c.o -MF CMakeFiles/latf-load.dir/zz_fastq-lex.c.o.d -o CMakeFiles/latf-load.dir/zz_fastq-lex.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_symlink_library ../../lib/libncbi-ngs.so.3.0.3 ../../lib/libncbi-ngs.so.3 ../../lib/libncbi-ngs.so +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:750: warning: "YY_BUF_SIZE" redefined + 750 | #define YY_BUF_SIZE 16777216 + | +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:204: note: this is the location of the previous definition + 204 | #define YY_BUF_SIZE 16384 + | +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: In function 'yylex': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1115:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 1115 | if ( ! yyg->yy_state_buf ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 1117 | if ( ! yyg->yy_state_buf ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1120:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 1120 | if ( ! yyg->yy_start ) + | ^~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: At top level: +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2409:24: warning: 'yy_fatal_error' defined but not used [-Wunused-function] + 2409 | static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner) + | ^~~~~~~~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2395:16: warning: 'yy_top_state' defined but not used [-Wunused-function] + 2395 | static int yy_top_state (yyscan_t yyscanner) + | ^~~~~~~~~~~~ +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1837:16: warning: 'input' defined but not used [-Wunused-function] + 1837 | static int input (yyscan_t yyscanner) + | ^~~~~ +[ 85%] Built target ncbi-ngs-shared make -f tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build.make tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build.make tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 84%] Building CXX object tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o +[ 85%] Building CXX object tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ngs-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o -MF CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o.d -o CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp -[ 84%] Linking CXX executable ../../../test-bin/Test_Align_samextract -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Align_samextract.dir/link.txt --verbose=1 -[ 84%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-reader.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-reader.c.o -MF CMakeFiles/latf-load.dir/fastq-reader.c.o.d -o CMakeFiles/latf-load.dir/fastq-reader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-reader.c -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o" -o ../../../test-bin/Test_Align_samextract -lsam-extract /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_symlink_library ../../lib/libncbi-ngs.so.3.0.3 ../../lib/libncbi-ngs.so.3 ../../lib/libncbi-ngs.so In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6371,98 +6458,69 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +/build/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp: In member function 'void NGS_Pileup::TargetReference::Process(std::ostream&)': +/build/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp:97:22: warning: unused variable 'next' [-Wunused-variable] + 97 | bool next = i -> nextPileup (); + | ^~~~ +[ 85%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/id2name.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/id2name.c.o -MF CMakeFiles/latf-load.dir/id2name.c.o.d -o CMakeFiles/latf-load.dir/id2name.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/id2name.c +[ 86%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-loader.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-loader.c.o -MF CMakeFiles/latf-load.dir/fastq-loader.c.o.d -o CMakeFiles/latf-load.dir/fastq-loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-loader.c +[ 86%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/loader-imp.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/loader-imp.c.o -MF CMakeFiles/latf-load.dir/loader-imp.c.o.d -o CMakeFiles/latf-load.dir/loader-imp.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/loader-imp.c +[ 86%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o -MF CMakeFiles/vdb-config.dir/util.cpp.o.d -o CMakeFiles/vdb-config.dir/util.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/util.cpp +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/loader-imp.c: In function 'WriteLoaderSignature': +/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/loader-imp.c:180:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 180 | rc = KLoaderMeta_Write(node, progName, __DATE__, "FASTQ", KAppVersion()); + | ^~~~~~~~ +[ 86%] Linking CXX executable ../../../test-bin/Test_Align_samextract +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Align_samextract.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o" -o ../../../test-bin/Test_Align_samextract -lsam-extract /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/bin/ld: CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o: in function `extract_buf(char const*, unsigned long, SAMExtractor**) [clone .constprop.0]': ./obj-x86_64-linux-gnu/test/internal/align/./test/internal/align/test-samextract.cpp:117: warning: the use of `tempnam' is dangerous, better use `mkstemp' -[ 84%] Built target ncbi-ngs-shared +[ 86%] Linking CXX executable ../../../test-bin/Test_Drivertool_FilePath +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_FilePath.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o" -o ../../../test-bin/Test_Drivertool_FilePath /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 86%] Built target Test_Align_samextract make -f tools/external/ref-variation/CMakeFiles/ref-variation.dir/build.make tools/external/ref-variation/CMakeFiles/ref-variation.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation/CMakeFiles/ref-variation.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/ref-variation/CMakeFiles/ref-variation.dir/build.make tools/external/ref-variation/CMakeFiles/ref-variation.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 84%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o +[ 86%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o -MF CMakeFiles/ref-variation.dir/common.cpp.o.d -o CMakeFiles/ref-variation.dir/common.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/common.cpp -[ 84%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o -MF CMakeFiles/sratools.dir/SDL-response.cpp.o.d -o CMakeFiles/sratools.dir/SDL-response.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/SDL-response.cpp -[ 84%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o -MF CMakeFiles/vdb-config.dir/util.cpp.o.d -o CMakeFiles/vdb-config.dir/util.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/util.cpp -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 84%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o -[ 84%] Built target Test_Align_samextract -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o -MF CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o.d -o CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o -c 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'/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/ref-variation/CMakeFiles/var-expand.dir/build.make tools/external/ref-variation/CMakeFiles/var-expand.dir/build +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/latf-load.dir/spot-assembler.c.o" "CMakeFiles/latf-load.dir/common-writer.c.o" "CMakeFiles/latf-load.dir/sequence-writer.c.o" "CMakeFiles/latf-load.dir/common-reader.c.o" "CMakeFiles/latf-load.dir/fastq-reader.c.o" "CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o" "CMakeFiles/latf-load.dir/zz_fastq-lex.c.o" "CMakeFiles/latf-load.dir/id2name.c.o" "CMakeFiles/latf-load.dir/fastq-loader.c.o" "CMakeFiles/latf-load.dir/loader-imp.c.o" -o ../../../bin/latf-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 84%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o -MF CMakeFiles/var-expand.dir/common.cpp.o.d -o CMakeFiles/var-expand.dir/common.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/common.cpp -[ 84%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfRetrier.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/PrfRetrier.c.o -MF CMakeFiles/prefetch.dir/PrfRetrier.c.o.d -o CMakeFiles/prefetch.dir/PrfRetrier.c.o -c 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-/build/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp: In member function 'void NGS_Pileup::TargetReference::Process(std::ostream&)': -/build/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp:97:22: warning: unused variable 'next' [-Wunused-variable] - 97 | bool next = i -> nextPileup (); - | ^~~~ -[ 84%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o -MF CMakeFiles/ref-variation.dir/helper.cpp.o.d -o CMakeFiles/ref-variation.dir/helper.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/helper.cpp -[ 85%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o -MF CMakeFiles/var-expand.dir/helper.cpp.o.d -o CMakeFiles/var-expand.dir/helper.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/helper.cpp -[ 85%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-lex.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-lex.c.o -MF CMakeFiles/latf-load.dir/zz_fastq-lex.c.o.d -o CMakeFiles/latf-load.dir/zz_fastq-lex.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:750: warning: "YY_BUF_SIZE" redefined - 750 | #define YY_BUF_SIZE 16777216 - | -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:204: note: this is the location of the previous definition - 204 | #define YY_BUF_SIZE 16384 - | -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: In function 'yylex': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1115:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 1115 | if ( ! yyg->yy_state_buf ) - | ^~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 1117 | if ( ! yyg->yy_state_buf ) - | ^~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1120:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 1120 | if ( ! yyg->yy_start ) - | ^~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: At top level: -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2409:24: warning: 'yy_fatal_error' defined but not used [-Wunused-function] - 2409 | static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner) - | ^~~~~~~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2395:16: warning: 'yy_top_state' defined but not used [-Wunused-function] - 2395 | static int yy_top_state (yyscan_t yyscanner) - | ^~~~~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1837:16: warning: 'input' defined but not used [-Wunused-function] - 1837 | static int input (yyscan_t yyscanner) - | ^~~~~ -[ 85%] Linking C executable ../../../bin/prefetch -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cmake -E cmake_link_script CMakeFiles/prefetch.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/prefetch.dir/kfile-no-q.c.o" CMakeFiles/prefetch.dir/PrfMain.c.o CMakeFiles/prefetch.dir/prefetch.c.o CMakeFiles/prefetch.dir/PrfRetrier.c.o CMakeFiles/prefetch.dir/PrfOutFile.c.o -o ../../../bin/prefetch ../../../ilib/libascp.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f prefetch.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv prefetch prefetch.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s prefetch.3.0.3 prefetch.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s prefetch.3 prefetch -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 prefetch-driver make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 85%] Linking CXX executable ../../../test-bin/Test_Drivertool_FilePath -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_FilePath.dir/link.txt --verbose=1 -[ 85%] Built target prefetch +[ 86%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o -MF CMakeFiles/var-expand.dir/common.cpp.o.d -o CMakeFiles/var-expand.dir/common.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/common.cpp +[ 86%] Built target Test_Drivertool_FilePath make -f tools/external/sra-search/CMakeFiles/sra-search.dir/build.make tools/external/sra-search/CMakeFiles/sra-search.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/CMakeFiles/sra-search.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o" -o ../../../test-bin/Test_Drivertool_FilePath /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-search/CMakeFiles/sra-search.dir/build.make tools/external/sra-search/CMakeFiles/sra-search.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 85%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/main.cpp.o +[ 86%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/main.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/main.cpp.o -MF CMakeFiles/sra-search.dir/main.cpp.o.d -o CMakeFiles/sra-search.dir/main.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/main.cpp -[ 86%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o -MF CMakeFiles/sratools.dir/tool-args.cpp.o.d -o CMakeFiles/sratools.dir/tool-args.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/tool-args.cpp +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f latf-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv latf-load latf-load.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s latf-load.3.0.3 latf-load.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s latf-load.3 latf-load +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 86%] Built target latf-load +[ 86%] Building C object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o -MF CMakeFiles/vdb-config.dir/vdb-config.c.o.d -o CMakeFiles/vdb-config.dir/vdb-config.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/vdb-config.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6473,18 +6531,31 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +[ 86%] Linking CXX executable ../../../bin/sratools +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/sratools.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/sratools.dir/sratools.cpp.o CMakeFiles/sratools.dir/config.cpp.o "CMakeFiles/sratools.dir/command-line.cpp.o" "CMakeFiles/sratools.dir/run-source.cpp.o" CMakeFiles/sratools.dir/proc.cpp.o CMakeFiles/sratools.dir/uuid.cpp.o CMakeFiles/sratools.dir/accession.cpp.o CMakeFiles/sratools.dir/service.cpp.o "CMakeFiles/sratools.dir/json-parse.cpp.o" "CMakeFiles/sratools.dir/SDL-response.cpp.o" "CMakeFiles/sratools.dir/tool-args.cpp.o" "CMakeFiles/sratools.dir/build-version.cpp.o" "CMakeFiles/sratools.dir/file-path.posix.cpp.o" CMakeFiles/sratools.dir/proc.posix.cpp.o -o ../../../bin/sratools /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 87%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o -MF CMakeFiles/var-expand.dir/helper.cpp.o.d -o CMakeFiles/var-expand.dir/helper.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/helper.cpp +[ 87%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o -MF CMakeFiles/ref-variation.dir/helper.cpp.o.d -o CMakeFiles/ref-variation.dir/helper.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/helper.cpp +[ 87%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfRetrier.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/PrfRetrier.c.o -MF CMakeFiles/prefetch.dir/PrfRetrier.c.o.d -o CMakeFiles/prefetch.dir/PrfRetrier.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/prefetch/PrfRetrier.c +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sratools.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sratools sratools.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sratools.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3 sratools make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 86%] Built target Test_Drivertool_FilePath +[ 87%] Built target sratools make -f tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 86%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o +[ 87%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o -MF CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o.d -o CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search.cpp -[ 86%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/id2name.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/id2name.c.o -MF CMakeFiles/latf-load.dir/id2name.c.o.d -o CMakeFiles/latf-load.dir/id2name.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/id2name.c +[ 87%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfOutFile.c.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/PrfOutFile.c.o -MF CMakeFiles/prefetch.dir/PrfOutFile.c.o.d -o CMakeFiles/prefetch.dir/PrfOutFile.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/prefetch/PrfOutFile.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6496,12 +6567,50 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 87%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-loader.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-loader.c.o -MF CMakeFiles/latf-load.dir/fastq-loader.c.o.d -o CMakeFiles/latf-load.dir/fastq-loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-loader.c [ 87%] Building CXX object tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/main.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ngs-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/main.cpp.o -MF CMakeFiles/ngs-pileup.dir/main.cpp.o.d -o CMakeFiles/ngs-pileup.dir/main.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/main.cpp -[ 87%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o -MF CMakeFiles/var-expand.dir/var-expand.cpp.o.d -o CMakeFiles/var-expand.dir/var-expand.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/var-expand.cpp +[ 87%] Linking C executable ../../../bin/prefetch +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cmake -E cmake_link_script CMakeFiles/prefetch.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/prefetch.dir/kfile-no-q.c.o" CMakeFiles/prefetch.dir/PrfMain.c.o CMakeFiles/prefetch.dir/prefetch.c.o CMakeFiles/prefetch.dir/PrfRetrier.c.o CMakeFiles/prefetch.dir/PrfOutFile.c.o -o ../../../bin/prefetch ../../../ilib/libascp.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 87%] Linking CXX executable ../../bin/gw-dumper +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -E cmake_link_script CMakeFiles/gw-dumper.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o" -o ../../bin/gw-dumper ../../ilib/libgeneral-writer.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f prefetch.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv prefetch prefetch.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s prefetch.3.0.3 prefetch.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s prefetch.3 prefetch +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 prefetch-driver +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 87%] Built target prefetch +make -f tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 87%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search-slow.cpp +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../searchbuffer.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../vdb-search.hpp:36, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/VdbSearchFixture.hpp:32, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search-slow.cpp:28: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 87%] Built target gw-dumper +make -f tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build.make tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build.make tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 87%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o -MF CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o.d -o CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-searchblock.cpp [ 87%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o -MF CMakeFiles/ref-variation.dir/ref-variation.cpp.o.d -o CMakeFiles/ref-variation.dir/ref-variation.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, @@ -6515,13 +6624,12 @@ from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/var-expand.cpp:8: + from /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:42: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 87%] Linking CXX executable ../../bin/gw-dumper -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -E cmake_link_script CMakeFiles/gw-dumper.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o" -o ../../bin/gw-dumper ../../ilib/libgeneral-writer.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 87%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o -MF CMakeFiles/var-expand.dir/var-expand.cpp.o.d -o CMakeFiles/var-expand.dir/var-expand.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/var-expand.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6533,10 +6641,29 @@ from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:42: + from /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/var-expand.cpp:8: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +[ 87%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive.cpp.o -MF CMakeFiles/vdb-config.dir/interactive.cpp.o.d -o CMakeFiles/vdb-config.dir/interactive.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/interactive.cpp +[ 88%] Linking CXX executable ../../../bin/ngs-pileup +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-pileup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o" "CMakeFiles/ngs-pileup.dir/main.cpp.o" -o ../../../bin/ngs-pileup ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f ngs-pileup.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv ngs-pileup ngs-pileup.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ngs-pileup.3.0.3 ngs-pileup.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ngs-pileup.3 ngs-pileup +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 88%] Built target ngs-pileup +make -f tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build.make tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build.make tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 88%] Building CXX object tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o -MF CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o.d -o CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats/pileup-stats.cpp In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/bxzstr.hpp:19, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parser.hpp:48, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parse.cpp:44: @@ -6544,8 +6671,6 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/strict_fstream.hpp:136:39: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 136 | catch (std::ios_base::failure e) {} | ^ -[ 87%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/loader-imp.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/loader-imp.c.o -MF CMakeFiles/latf-load.dir/loader-imp.c.o.d -o CMakeFiles/latf-load.dir/loader-imp.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/loader-imp.c In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/bxzstr.hpp:20: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/compression_types.hpp: In function 'bxz::Compression bxz::detect_type(char*, char*)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/compression_types.hpp:33:19: warning: unused variable 'b3' [-Wunused-variable] @@ -6557,48 +6682,6 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/compression_types.hpp:35:19: warning: unused variable 'b5' [-Wunused-variable] 35 | unsigned char b5 = *reinterpret_cast< unsigned char * >(in_buff_start + 5); | ^~ -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/loader-imp.c: In function 'WriteLoaderSignature': -/build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/loader-imp.c:180:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 180 | rc = KLoaderMeta_Write(node, progName, __DATE__, "FASTQ", KAppVersion()); - | ^~~~~~~~ -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 87%] Built target gw-dumper -make -f tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 87%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search-slow.cpp -[ 87%] Linking C executable ../../../bin/latf-load -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/latf-load.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/latf-load.dir/spot-assembler.c.o" "CMakeFiles/latf-load.dir/common-writer.c.o" "CMakeFiles/latf-load.dir/sequence-writer.c.o" "CMakeFiles/latf-load.dir/common-reader.c.o" "CMakeFiles/latf-load.dir/fastq-reader.c.o" "CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o" "CMakeFiles/latf-load.dir/zz_fastq-lex.c.o" "CMakeFiles/latf-load.dir/id2name.c.o" "CMakeFiles/latf-load.dir/fastq-loader.c.o" "CMakeFiles/latf-load.dir/loader-imp.c.o" -o ../../../bin/latf-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../searchbuffer.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../vdb-search.hpp:36, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/VdbSearchFixture.hpp:32, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search-slow.cpp:28: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f latf-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv latf-load latf-load.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s latf-load.3.0.3 latf-load.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s latf-load.3 latf-load -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 87%] Built target latf-load -make -f tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build.make tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build.make tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 87%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o -MF CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o.d -o CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-searchblock.cpp /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp: In instantiation of 'int NSRefVariation::find_alignment_in_pileup_db(const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, size_t, TLock*, size_t, coverage_info*, size_t) [with TLock = KProc::CKLock; size_t = long unsigned int]': /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:853:47: required from 'void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, TLock*, size_t, coverage_info*) [with TLock = KProc::CKLock; size_t = long unsigned int]' /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:893:43: required from 'void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const std::vector*, TLock*, size_t) [with TLock = KProc::CKLock; size_t = long unsigned int]' @@ -6613,42 +6696,40 @@ /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:933:51: required from 'void NSRefVariation::find_alignments(const char*, const std::vector*, TLock*, size_t, const CInputRuns*, KApp::CProgressBar*) [with TLock = CNoMutex; size_t = long unsigned int]' /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:1051:29: required from here /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:570:28: warning: unused variable 'allele_size' [-Wunused-variable] -[ 87%] Linking CXX executable ../../../bin/var-expand +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats/pileup-stats.cpp:29: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 88%] Linking CXX executable ../../../bin/var-expand cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/cmake -E cmake_link_script CMakeFiles/var-expand.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/var-expand.dir/common.cpp.o" "CMakeFiles/var-expand.dir/helper.cpp.o" "CMakeFiles/var-expand.dir/var-expand.cpp.o" -o ../../../bin/var-expand ../../../ilib/libtk-version.a -lkapp ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a -[ 88%] Linking CXX executable ../../../bin/ngs-pileup -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-pileup.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o" "CMakeFiles/ngs-pileup.dir/main.cpp.o" -o ../../../bin/ngs-pileup ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a -[ 88%] Linking CXX executable ../../../test-bin/Test_Drivertool_SDLResponse -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_SDLResponse.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o" -o ../../../test-bin/Test_Drivertool_SDLResponse +[ 88%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/searchblock.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/searchblock.cpp.o -MF CMakeFiles/sra-search.dir/searchblock.cpp.o.d -o CMakeFiles/sra-search.dir/searchblock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f var-expand.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv var-expand var-expand.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s var-expand.3.0.3 var-expand.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s var-expand.3 var-expand make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target var-expand -make -f tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build.make tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f ngs-pileup.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv ngs-pileup ngs-pileup.3.0.3 -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build.make tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ngs-pileup.3.0.3 ngs-pileup.3 -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ngs-pileup.3 ngs-pileup -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 88%] Building CXX object tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o -MF CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o.d -o CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats/pileup-stats.cpp -[ 88%] Built target ngs-pileup make -f test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/build.make test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/build.make test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 88%] Building CXX object test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/ngs/testy-the-bear\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o -MF CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o.d -o CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6660,19 +6741,12 @@ from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats/pileup-stats.cpp:29: + from /build/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp:1: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 88%] Building CXX object test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/ngs/testy-the-bear\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o -MF CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o.d -o CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp -[ 88%] Built target Test_Drivertool_SDLResponse -make -f test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build.make test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/ngs-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build.make test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 89%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o -MF CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6683,16 +6757,28 @@ from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp:1: + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 88%] Building CXX object test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o -MF CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o.d -o CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/ngs-pileup/test-ngs-pileup.cpp -[ 88%] Linking CXX executable ../../../test-bin/test-vdb-config-model +[ 89%] Linking CXX executable ../../../test-bin/test-vdb-config-model cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-vdb-config-model.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o" -o ../../../test-bin/test-vdb-config-model /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +In file included from /build/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp:3: +/usr/include/ncbi-vdb/kfc/ctx.h:68:19: warning: 's_src_loc' defined but not used [-Wunused-variable] + 68 | static KSourceLoc s_src_loc = { __mod__, __file__, __fext__ }; + | ^~~~~~~~~ +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 89%] Built target test-vdb-config-model +make -f test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build.make test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/ngs-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build.make test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 89%] Building CXX object test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o -MF CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o.d -o CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/ngs-pileup/test-ngs-pileup.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6709,16 +6795,25 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +[ 89%] Linking CXX executable ../../../test-bin/Test_Drivertool_SDLResponse +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_SDLResponse.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o" -o ../../../test-bin/Test_Drivertool_SDLResponse +[ 90%] Linking CXX executable ../../../../test-bin/testy-the-bear +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear && /usr/bin/cmake -E cmake_link_script CMakeFiles/testy-the-bear.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o" -o ../../../../test-bin/testy-the-bear /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a ../../../../lib/libncbi-ngs-c++.a ../../../../lib/libncbi-ngs.a ../../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 90%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o -MF CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp +[ 90%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o -MF CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 88%] Built target test-vdb-config-model +[ 90%] Built target Test_Drivertool_SDLResponse make -f test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/build.make test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/internal/align /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/build.make test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 88%] Building CXX object test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/align\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/ext -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/../ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -MF CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o.d -o CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/internal/align/pileup_estimator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6729,37 +6824,22 @@ from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/test/internal/align/pileup_estimator.cpp:52: + from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.hpp:30, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -In file included from /build/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp:3: -/usr/include/ncbi-vdb/kfc/ctx.h:68:19: warning: 's_src_loc' defined but not used [-Wunused-variable] - 68 | static KSourceLoc s_src_loc = { __mod__, __file__, __fext__ }; - | ^~~~~~~~~ -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/external/ngs-pileup/ngs-pileup.cpp: In member function 'void NGS_Pileup::TargetReference::Process(std::ostream&)': -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/external/ngs-pileup/ngs-pileup.cpp:97:22: warning: unused variable 'next' [-Wunused-variable] - 97 | bool next = i -> nextPileup (); - | ^~~~ -[ 88%] Building C object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o -MF CMakeFiles/vdb-config.dir/vdb-config.c.o.d -o CMakeFiles/vdb-config.dir/vdb-config.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/vdb-config.c -[ 89%] Linking CXX executable ../../../../test-bin/testy-the-bear -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear && /usr/bin/cmake -E cmake_link_script CMakeFiles/testy-the-bear.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o" -o ../../../../test-bin/testy-the-bear /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a ../../../../lib/libncbi-ngs-c++.a ../../../../lib/libncbi-ngs.a ../../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 89%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o -MF CMakeFiles/sratools.dir/build-version.cpp.o.d -o CMakeFiles/sratools.dir/build-version.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/build-version.cpp -[ 89%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/searchblock.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/searchblock.cpp.o -MF CMakeFiles/sra-search.dir/searchblock.cpp.o.d -o CMakeFiles/sra-search.dir/searchblock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 89%] Built target testy-the-bear +[ 90%] Built target testy-the-bear make -f ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/DependInfo.cmake --color= +[ 90%] Building CXX object test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/align\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/ext -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/../ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -MF CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o.d -o CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/internal/align/pileup_estimator.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 89%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/FragTest.cpp.o +[ 90%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/FragTest.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/FragTest.cpp.o -MF CMakeFiles/FragTest.dir/FragTest.cpp.o.d -o CMakeFiles/FragTest.dir/FragTest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/FragTest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, @@ -6772,14 +6852,10 @@ from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/FragTest.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/test/internal/align/pileup_estimator.cpp:52: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 90%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o -MF CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp -[ 90%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o -MF CMakeFiles/sratools.dir/file-path.posix.cpp.o.d -o CMakeFiles/sratools.dir/file-path.posix.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/file-path.posix.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6790,47 +6866,51 @@ from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/FragTest.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 90%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o -MF CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/external/ngs-pileup/ngs-pileup.cpp: In member function 'void NGS_Pileup::TargetReference::Process(std::ostream&)': +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/external/ngs-pileup/ngs-pileup.cpp:97:22: warning: unused variable 'next' [-Wunused-variable] + 97 | bool next = i -> nextPileup (); + | ^~~~ +[ 90%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o -MF CMakeFiles/vdb-config.dir/interactive2.cpp.o.d -o CMakeFiles/vdb-config.dir/interactive2.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/interactive2.cpp [ 90%] Linking CXX executable ../../../bin/pileup-stats -[ 90%] Linking CXX executable ../../../test-bin/FragTest -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragTest.dir/link.txt --verbose=1 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats && /usr/bin/cmake -E cmake_link_script CMakeFiles/pileup-stats.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/FragTest.dir/FragTest.cpp.o -o ../../../test-bin/FragTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o" -o ../../../bin/pileup-stats ../../../ilib/libgeneral-writer.a ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -[ 90%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive.cpp.o -MF CMakeFiles/vdb-config.dir/interactive.cpp.o.d -o CMakeFiles/vdb-config.dir/interactive.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/interactive.cpp +[ 90%] Linking CXX executable ../../../../test-bin/test-searchblock +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-searchblock.dir/link.txt --verbose=1 +[ 91%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o" "CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o" -o ../../../../test-bin/test-searchblock ../../../../ilib/libngs-vdb.a ../../../../lib/libncbi-ngs.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o -MF CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o.d -o CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/vdb-config-model.cpp +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pileup-stats.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pileup-stats pileup-stats.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pileup-stats.3.0.3 pileup-stats.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pileup-stats.3 pileup-stats make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 90%] Linking CXX executable ../../../bin/ref-variation -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/cmake -E cmake_link_script CMakeFiles/ref-variation.dir/link.txt --verbose=1 -[ 90%] Built target FragTest +[ 91%] Built target pileup-stats make -f ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/ref-variation.dir/common.cpp.o" "CMakeFiles/ref-variation.dir/helper.cpp.o" "CMakeFiles/ref-variation.dir/ref-variation.cpp.o" -o ../../../bin/ref-variation ../../../ilib/libtk-version.a -lkapp ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pileup-stats.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pileup-stats pileup-stats.3.0.3 -[ 90%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/AlignTest.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/AlignTest.cpp.o -MF CMakeFiles/AlignTest.dir/AlignTest.cpp.o.d -o CMakeFiles/AlignTest.dir/AlignTest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/AlignTest.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pileup-stats.3.0.3 pileup-stats.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pileup-stats.3 pileup-stats make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 90%] Built target pileup-stats +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 91%] Built target test-searchblock make -f ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/DependInfo.cmake --color= +[ 91%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/AlignTest.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/AlignTest.cpp.o -MF CMakeFiles/AlignTest.dir/AlignTest.cpp.o.d -o CMakeFiles/AlignTest.dir/AlignTest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/AlignTest.cpp +[ 91%] Linking CXX executable ../../../test-bin/FragTest +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragTest.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 90%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/FragTest.dir/FragTest.cpp.o -o ../../../test-bin/FragTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 91%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o -MF CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o.d -o CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/AlignSliceTest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, @@ -6862,22 +6942,11 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f ref-variation.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv ref-variation ref-variation.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ref-variation.3.0.3 ref-variation.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ref-variation.3 ref-variation +[ 91%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o -MF CMakeFiles/sra-search.dir/referencematchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/referencematchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 90%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o -MF CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp -[ 90%] Built target ref-variation +[ 91%] Built target FragTest make -f ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/PileupTest.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/PileupTest.cpp.o -MF CMakeFiles/PileupTest.dir/PileupTest.cpp.o.d -o CMakeFiles/PileupTest.dir/PileupTest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/PileupTest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6888,12 +6957,19 @@ from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.hpp:30, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp:27: + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 92%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/PileupTest.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/PileupTest.cpp.o -MF CMakeFiles/PileupTest.dir/PileupTest.cpp.o.d -o CMakeFiles/PileupTest.dir/PileupTest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/PileupTest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6909,19 +6985,37 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 91%] Linking CXX executable ../../../../test-bin/test-searchblock -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-searchblock.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o" "CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o" -o ../../../../test-bin/test-searchblock ../../../../ilib/libngs-vdb.a ../../../../lib/libncbi-ngs.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a +[ 92%] Linking CXX executable ../../../bin/ref-variation +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/cmake -E cmake_link_script CMakeFiles/ref-variation.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/ref-variation.dir/common.cpp.o" "CMakeFiles/ref-variation.dir/helper.cpp.o" "CMakeFiles/ref-variation.dir/ref-variation.cpp.o" -o ../../../bin/ref-variation ../../../ilib/libtk-version.a -lkapp ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f ref-variation.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv ref-variation ref-variation.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ref-variation.3.0.3 ref-variation.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ref-variation.3 ref-variation make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target test-searchblock +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In function 'std::string ReverseComplementDNA(const std::string&)': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:94:32: warning: array subscript has type 'char' [-Wchar-subscripts] + 94 | char ch = complement [ *i ]; + | ^~ +[ 92%] Built target ref-variation make -f ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/DependInfo.cmake --color= +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In member function 'virtual MatchIterator* ReferenceSearch::NextIterator()': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:574:33: warning: catching polymorphic type 'class ngs::ErrorMsg' by value [-Wcatch-value=] + 574 | catch ( ngs :: ErrorMsg ex ) + | ^~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/RefTest.cpp.o +[ 92%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/RefTest.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/RefTest.cpp.o -MF CMakeFiles/RefTest.dir/RefTest.cpp.o.d -o CMakeFiles/RefTest.dir/RefTest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/RefTest.cpp +[ 92%] Linking CXX executable ../../../test-bin/AlignSliceTest +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/AlignSliceTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o -o ../../../test-bin/AlignSliceTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 92%] Linking CXX executable ../../../test-bin/AlignTest +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/AlignTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/AlignTest.dir/AlignTest.cpp.o -o ../../../test-bin/AlignTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6937,50 +7031,26 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 91%] Linking CXX executable ../../../test-bin/AlignTest -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/AlignTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/AlignTest.dir/AlignTest.cpp.o -o ../../../test-bin/AlignTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 91%] Linking CXX executable ../../../test-bin/AlignSliceTest -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/AlignSliceTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o -o ../../../test-bin/AlignSliceTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 91%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o -MF CMakeFiles/sratools.dir/proc.posix.cpp.o.d -o CMakeFiles/sratools.dir/proc.posix.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o -MF CMakeFiles/sra-search.dir/referencematchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/referencematchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp -[ 91%] Built target AlignTest +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 92%] Built target AlignTest make -f ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/depend +[ 92%] Built target AlignSliceTest +make -f libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -[ 91%] Linking CXX executable ../../../test-bin/PileupTest -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/PileupTest.dir/link.txt --verbose=1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -MF CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o.d -o CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/DumpReferenceFASTA.cpp -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/PileupTest.dir/PileupTest.cpp.o -o ../../../test-bin/PileupTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target AlignSliceTest -make -f libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/depend +make -f libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/DependInfo.cmake --color= +[ 92%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -MF CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o.d -o CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/DumpReferenceFASTA.cpp +[ 92%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/ngstest.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/ngstest.cpp.o -MF CMakeFiles/test-ngs.dir/ngstest.cpp.o.d -o CMakeFiles/test-ngs.dir/ngstest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -6996,11 +7066,9 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/ngstest.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/ngstest.cpp.o -MF CMakeFiles/test-ngs.dir/ngstest.cpp.o.d -o CMakeFiles/test-ngs.dir/ngstest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest.cpp +[ 92%] Linking CXX executable ../../../test-bin/PileupTest +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/PileupTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/PileupTest.dir/PileupTest.cpp.o -o ../../../test-bin/PileupTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -7008,79 +7076,77 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +[ 92%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o -MF CMakeFiles/sra-search.dir/vdb-search.cpp.o.d -o CMakeFiles/sra-search.dir/vdb-search.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target PileupTest +[ 92%] Built target PileupTest make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o +[ 92%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o -MF CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o.d -o CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sra.cpp -[ 91%] Linking CXX executable ../../../test-bin/RefTest +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp:29: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 92%] Linking CXX executable ../../../test-bin/RefTest cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/RefTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/RefTest.dir/RefTest.cpp.o -o ../../../test-bin/RefTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In function 'std::string ReverseComplementDNA(const std::string&)': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:94:32: warning: array subscript has type 'char' [-Wchar-subscripts] - 94 | char ch = complement [ *i ]; - | ^~ -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In member function 'virtual MatchIterator* ReferenceSearch::NextIterator()': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:574:33: warning: catching polymorphic type 'class ngs::ErrorMsg' by value [-Wcatch-value=] - 574 | catch ( ngs :: ErrorMsg ex ) - | ^~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target RefTest +[ 92%] Built target RefTest make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp: In member function 'POSIX::Process::ExitStatus POSIX::Process::wait() const': -/build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp:246:28: warning: 'void std::unexpected()' is deprecated [-Wdeprecated-declarations] - 246 | std::unexpected(); - | ~~~~~~~~~~~~~~~^~ -In file included from /usr/include/c++/12/ios:39, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp:42: -/usr/include/c++/12/exception:109:8: note: declared here - 109 | void unexpected() __attribute__ ((__noreturn__)); - | ^~~~~~~~~~ -[ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o +[ 92%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o -MF CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o.d -o CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sradb.cpp -[ 91%] Linking CXX executable ../../../test-bin/DumpReferenceFASTA -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/DumpReferenceFASTA.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -o ../../../test-bin/DumpReferenceFASTA ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 91%] Linking CXX executable ../../../test-bin/test-ngs +[ 92%] Linking CXX executable ../../../test-bin/test-ngs cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs.dir/ngstest.cpp.o" -o ../../../test-bin/test-ngs -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +[ 92%] Linking CXX executable ../../../test-bin/DumpReferenceFASTA +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/DumpReferenceFASTA.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -o ../../../test-bin/DumpReferenceFASTA ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target DumpReferenceFASTA +[ 92%] Built target test-ngs make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o -[ 91%] Built target test-ngs -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o -MF CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 92%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o -MF CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o.d -o CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1.cpp +[ 92%] Built target DumpReferenceFASTA make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/depend -[ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/DependInfo.cmake --color= -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o -MF CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o.d -o CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o -[ 91%] Linking CXX executable ../../../test-bin/Test_Ngs_Pileup +make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/DependInfo.cmake --color= +[ 92%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o -MF CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o.d -o CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_readcollection.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Ngs_Pileup.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o" -o ../../../test-bin/Test_Ngs_Pileup ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 92%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o -MF CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o.d -o CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp +[ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -7091,44 +7157,26 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 91%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o -MF CMakeFiles/vdb-config.dir/interactive2.cpp.o.d -o CMakeFiles/vdb-config.dir/interactive2.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/interactive2.cpp -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target Test_Ngs_Pileup -make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o -[ 91%] Linking CXX executable ../../../test-bin/SlowTest_Align_estimator -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o -MF CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o.d -o CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/SlowTest_Align_estimator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -o ../../../test-bin/SlowTest_Align_estimator ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sradb.cpp: In function 'rc_t KMain(int, char**)': /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sradb.cpp:864:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 864 | putenv("NCBI_VDB_QUALITY=R"); | ^~~~~~~~~~~~~~~~~~~~ +[ 92%] Linking CXX executable ../../../test-bin/Test_Ngs_Pileup +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Ngs_Pileup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o" -o ../../../test-bin/Test_Ngs_Pileup ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +[ 92%] Linking CXX executable ../../../bin/vdb-config +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-config.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-config.dir/configure.cpp.o" "CMakeFiles/vdb-config.dir/util.cpp.o" "CMakeFiles/vdb-config.dir/vdb-config.c.o" "CMakeFiles/vdb-config.dir/interactive.cpp.o" "CMakeFiles/vdb-config.dir/interactive2.cpp.o" "CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o" -o ../../../bin/vdb-config ../../../ilib/libtui_cpp.a ../../../ilib/libtui.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target SlowTest_Align_estimator +[ 92%] Built target Test_Ngs_Pileup make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o +[ 92%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o -MF CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o.d -o CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp -[ 91%] Linking CXX executable ../../../bin/sratools -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/sratools.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/sratools.dir/sratools.cpp.o CMakeFiles/sratools.dir/config.cpp.o "CMakeFiles/sratools.dir/command-line.cpp.o" "CMakeFiles/sratools.dir/run-source.cpp.o" CMakeFiles/sratools.dir/proc.cpp.o CMakeFiles/sratools.dir/uuid.cpp.o CMakeFiles/sratools.dir/accession.cpp.o CMakeFiles/sratools.dir/service.cpp.o "CMakeFiles/sratools.dir/json-parse.cpp.o" "CMakeFiles/sratools.dir/SDL-response.cpp.o" "CMakeFiles/sratools.dir/tool-args.cpp.o" "CMakeFiles/sratools.dir/build-version.cpp.o" "CMakeFiles/sratools.dir/file-path.posix.cpp.o" CMakeFiles/sratools.dir/proc.posix.cpp.o -o ../../../bin/sratools /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o -MF CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp -[ 92%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o -MF CMakeFiles/sra-search.dir/vdb-search.cpp.o.d -o CMakeFiles/sra-search.dir/vdb-search.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp -[ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceWindow_Slice_Filtered::Instance::test_method()': /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:591:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 591 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) @@ -7149,50 +7197,75 @@ /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:740:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 740 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) | ^ -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp:29: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp:29: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sratools.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sratools sratools.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sratools.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3 sratools +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-config.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-config vdb-config.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-config.3.0.3 vdb-config.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-config.3 vdb-config +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cmake -E copy /usr/include/ncbi-vdb/kfg/ncbi/default.kfg /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/ncbi/default.kfg make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 92%] Built target sratools +[ 92%] Linking CXX executable ../../../bin/sra-search +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-search.dir/link.txt --verbose=1 +[ 92%] Built target vdb-config make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-search.dir/main.cpp.o" "CMakeFiles/sra-search.dir/searchblock.cpp.o" "CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o" "CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o" "CMakeFiles/sra-search.dir/referencematchiterator.cpp.o" "CMakeFiles/sra-search.dir/vdb-search.cpp.o" -o ../../../bin/sra-search ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libtk-version.a -Wl,-Bstatic -lkapp -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 92%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o -MF CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o.d -o CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_reference.cpp +[ 92%] Linking CXX executable ../../../test-bin/SlowTest_Align_estimator +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/SlowTest_Align_estimator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -o ../../../test-bin/SlowTest_Align_estimator ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-search.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-search sra-search.3.0.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-search.3.0.3 sra-search.3 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-search.3 sra-search +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 92%] Built target sra-search +make -f libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 92%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o -MF CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o.d -o CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_fragmentblob.cpp +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 92%] Built target SlowTest_Align_estimator +make -f libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 92%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o -MF CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o.d -o CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_referenceblob.cpp /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp: In member function 'void CSRA1_PileupIterator_AccessAfterNext_PileupGetReferenceBase::Instance::test_method()': /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp:191:10: warning: unused variable 'base' [-Wunused-variable] 191 | char base = NGS_PileupGetReferenceBase ( m_pileup, ctx ); | ^~~~ -[ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp: In member function 'void CSRA1_PileupIteratorSlice_AccessAfterNext_PileupGetReferenceBase::Instance::test_method()': /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp:386:10: warning: unused variable 'base' [-Wunused-variable] 386 | char base = NGS_PileupGetReferenceBase ( m_pileup, ctx ); | ^~~~ +[ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp +[ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o -MF CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp:29: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 93%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -7209,8 +7282,8 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp +[ 93%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -7226,8 +7299,15 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp +[ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o -MF CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp +[ 94%] Linking CXX executable ../../../../test-bin/test-general-loader +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-general-loader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o" "CMakeFiles/test-general-loader.dir/testsource.cpp.o" -o ../../../../test-bin/test-general-loader ../../../../ilib/libgeneral-writer.a -lkapp -lktst ../../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm +[ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp +[ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -7244,40 +7324,6 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 93%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o -MF CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o.d -o CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/vdb-config-model.cpp -[ 93%] Linking CXX executable ../../../bin/sra-search -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-search.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-search.dir/main.cpp.o" "CMakeFiles/sra-search.dir/searchblock.cpp.o" "CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o" "CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o" "CMakeFiles/sra-search.dir/referencematchiterator.cpp.o" "CMakeFiles/sra-search.dir/vdb-search.cpp.o" -o ../../../bin/sra-search ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libtk-version.a -Wl,-Bstatic -lkapp -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a -[ 93%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-search.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-search sra-search.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-search.3.0.3 sra-search.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-search.3 sra-search -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In function 'std::string ReverseComplementDNA(const std::string&)': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:94:32: warning: array subscript has type 'char' [-Wchar-subscripts] - 94 | char ch = complement [ *i ]; - | ^~ -[ 93%] Built target sra-search -make -f libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/depend -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In member function 'virtual MatchIterator* ReferenceSearch::NextIterator()': -/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:574:33: warning: catching polymorphic type 'class ngs::ErrorMsg' by value [-Wcatch-value=] - 574 | catch ( ngs :: ErrorMsg ex ) - | ^~ -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 93%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o -MF CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o.d -o CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_fragmentblob.cpp -[ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp -make -f libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/DependInfo.cmake --color= In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -7295,58 +7341,25 @@ 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o -MF CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o.d -o CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_referenceblob.cpp -[ 94%] Linking CXX executable ../../../../test-bin/test-sra-search -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sra-search.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o" "CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o" "CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o" "CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o" "CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o" "CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o" -o ../../../../test-bin/test-sra-search ../../../../ilib/libngs-vdb.a ../../../../lib/libncbi-ngs.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a -[ 94%] Linking CXX executable ../../../bin/vdb-config -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-config.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-config.dir/configure.cpp.o" "CMakeFiles/vdb-config.dir/util.cpp.o" "CMakeFiles/vdb-config.dir/vdb-config.c.o" "CMakeFiles/vdb-config.dir/interactive.cpp.o" "CMakeFiles/vdb-config.dir/interactive2.cpp.o" "CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o" -o ../../../bin/vdb-config ../../../ilib/libtui_cpp.a ../../../ilib/libtui.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -[ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-config.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-config vdb-config.3.0.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-config.3.0.3 vdb-config.3 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-config.3 vdb-config -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cmake -E copy /usr/include/ncbi-vdb/kfg/ncbi/default.kfg /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/ncbi/default.kfg -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 94%] Built target test-sra-search +[ 94%] Built target test-general-loader make -f libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/DependInfo.cmake --color= -[ 94%] Built target vdb-config -make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/depend -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/DependInfo.cmake --color= -In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, - from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp:27: -/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] - 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" - | make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o -MF CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o.d -o CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_byteblob.cpp -[ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o -MF CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o.d -o CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRAtest.cpp +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In function 'std::string ReverseComplementDNA(const std::string&)': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:94:32: warning: array subscript has type 'char' [-Wchar-subscripts] + 94 | char ch = complement [ *i ]; + | ^~ +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In member function 'virtual MatchIterator* ReferenceSearch::NextIterator()': +/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:574:33: warning: catching polymorphic type 'class ngs::ErrorMsg' by value [-Wcatch-value=] + 574 | catch ( ngs :: ErrorMsg ex ) + | ^~ +[ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -7357,14 +7370,13 @@ from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, - from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngsfixture.hpp:36, - from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRAtest.cpp:31: + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, + from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp +[ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, @@ -7392,11 +7404,37 @@ [ 94%] Linking CXX executable ../../../../test-bin/test-sra-search-slow cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sra-search-slow.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o" -o ../../../../test-bin/test-sra-search-slow ../../../../ilib/libngs-vdb.a ../../../../lib/libncbi-ngs.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a -[ 94%] Linking CXX executable ../../../../test-bin/test-general-loader -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-general-loader.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o" "CMakeFiles/test-general-loader.dir/testsource.cpp.o" -o ../../../../test-bin/test-general-loader ../../../../ilib/libgeneral-writer.a -lkapp -lktst ../../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 94%] Built target test-general-loader +[ 94%] Built target test-sra-search-slow +make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/depend +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o -MF CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o.d -o CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRAtest.cpp +In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, + from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngsfixture.hpp:36, + from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRAtest.cpp:31: +/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] + 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" + | +[ 94%] Linking CXX executable ../../../../test-bin/test-sra-search +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sra-search.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o" "CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o" "CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o" "CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o" "CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o" "CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o" -o ../../../../test-bin/test-sra-search ../../../../ilib/libngs-vdb.a ../../../../lib/libncbi-ngs.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 94%] Built target test-sra-search make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/DependInfo.cmake --color= @@ -7421,8 +7459,15 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | +[ 94%] Linking CXX executable ../../../test-bin/test-fragmentblob +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-fragmentblob.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o" -o ../../../test-bin/test-fragmentblob -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +/build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp: In function 'rc_t KMain(int, char**)': +/build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp:530:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 530 | putenv("NCBI_VDB_QUALITY=R"); + | ^~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 94%] Built target test-sra-search-slow +[ 94%] Built target test-fragmentblob make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/DependInfo.cmake --color= @@ -7447,10 +7492,6 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -/build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp: In function 'rc_t KMain(int, char**)': -/build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp:530:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 530 | putenv("NCBI_VDB_QUALITY=R"); - | ^~~~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX executable ../../../test-bin/test-byteblob cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-byteblob.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o" -o ../../../test-bin/test-byteblob -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a @@ -7480,11 +7521,11 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 94%] Linking CXX executable ../../../test-bin/test-fragmentblob -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-fragmentblob.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o" -o ../../../test-bin/test-fragmentblob -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +[ 94%] Linking CXX executable ../../../test-bin/test-ngs_csra1_pileup +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_pileup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o" -o ../../../test-bin/test-ngs_csra1_pileup -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 94%] Built target test-fragmentblob +[ 94%] Built target test-ngs_csra1_pileup make -f libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/DependInfo.cmake --color= @@ -7509,43 +7550,61 @@ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | -[ 95%] Linking CXX executable ../../../test-bin/test-ngs_csra1_pileup -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_pileup.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o" -o ../../../test-bin/test-ngs_csra1_pileup -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 95%] Built target test-ngs_csra1_pileup [ 95%] Linking CXX executable ../../../test-bin/test-ngs_csra1_refwin cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_refwin.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o" -o ../../../test-bin/test-ngs_csra1_refwin -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target test-ngs_csra1_refwin -[ 95%] Linking CXX executable ../../../test-bin/test-ngs_sra_c++ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sra_c++.dir/link.txt --verbose=1 +[ 95%] Linking CXX executable ../../../test-bin/test-referenceblob +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-referenceblob.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o" -o ../../../test-bin/test-referenceblob -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 95%] Built target test-referenceblob [ 95%] Linking CXX executable ../../../test-bin/test-ngs_reference cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_reference.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o" -o ../../../test-bin/test-ngs_sra_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o" -o ../../../test-bin/test-ngs_reference -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +[ 96%] Linking CXX executable ../../../test-bin/test-ngs_csra1_readcollection +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_readcollection.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o" -o ../../../test-bin/test-ngs_csra1_readcollection -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 95%] Built target test-ngs_reference +[ 96%] Built target test-ngs_reference +[ 96%] Linking CXX executable ../../../test-bin/test-ngs_sradb +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sradb.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o" -o ../../../test-bin/test-ngs_sradb -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 95%] Built target test-ngs_sra_c++ -[ 95%] Linking CXX executable ../../../test-bin/test-ngs_csra1pileup++ +[ 96%] Built target test-ngs_csra1_readcollection +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target test-ngs_sradb +[ 96%] Linking CXX executable ../../../test-bin/test-ngs_csra1pileup++ cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1pileup++.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o" -o ../../../test-bin/test-ngs_csra1pileup++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 95%] Built target test-ngs_csra1pileup++ -[ 96%] Linking CXX executable ../../../test-bin/test-ngs_csra1_readcollection -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_readcollection.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o" -o ../../../test-bin/test-ngs_csra1_readcollection -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a -[ 96%] Linking C static library ../../ilib/libvdb-sqlite.a +[ 96%] Built target test-ngs_csra1pileup++ +[ 97%] Linking CXX executable ../../../test-bin/test-ngs_sra +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sra.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o" -o ../../../test-bin/test-ngs_sra -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +[ 97%] Linking CXX executable ../../../test-bin/test-ngs_sra_c++ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sra_c++.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o" -o ../../../test-bin/test-ngs_sra_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target test-ngs_sra +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target test-ngs_sra_c++ +[ 97%] Linking CXX executable ../../../test-bin/test-ngs_csra1 +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o" -o ../../../test-bin/test-ngs_csra1 -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target test-ngs_csra1 +[ 97%] Linking CXX executable ../../../test-bin/test-ngs_sradb_c++ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sradb_c++.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o" -o ../../../test-bin/test-ngs_sradb_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +[ 97%] Linking C static library ../../ilib/libvdb-sqlite.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cmake -P CMakeFiles/vdb-sqlite.dir/cmake_clean_target.cmake cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-sqlite.dir/link.txt --verbose=1 /usr/bin/ar qc ../../ilib/libvdb-sqlite.a "CMakeFiles/vdb-sqlite.dir/sqlite3.c.o" "CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o" -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target test-ngs_csra1_readcollection /usr/bin/ranlib ../../ilib/libvdb-sqlite.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target vdb-sqlite +[ 97%] Built target vdb-sqlite make -f tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/build.make tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/depend make -f tools/internal/vdb-sql/CMakeFiles/fastconv.dir/build.make tools/internal/vdb-sql/CMakeFiles/fastconv.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' @@ -7554,62 +7613,39 @@ cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql/CMakeFiles/fastconv.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/build.make tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/build -make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-sql/CMakeFiles/fastconv.dir/build.make tools/internal/vdb-sql/CMakeFiles/fastconv.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 96%] Building C object tools/internal/vdb-sql/CMakeFiles/fastconv.dir/fastconv.c.o -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-sql\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-sql/CMakeFiles/fastconv.dir/fastconv.c.o -MF CMakeFiles/fastconv.dir/fastconv.c.o.d -o CMakeFiles/fastconv.dir/fastconv.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql/fastconv.c -[ 97%] Building C object tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/vdb_shell.c.o +[ 98%] Building C object tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/vdb_shell.c.o +[ 98%] Building C object tools/internal/vdb-sql/CMakeFiles/fastconv.dir/fastconv.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-sql\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/vdb_shell.c.o -MF CMakeFiles/vdb-sql.dir/vdb_shell.c.o.d -o CMakeFiles/vdb-sql.dir/vdb_shell.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql/vdb_shell.c -[ 97%] Linking CXX executable ../../../test-bin/test-referenceblob -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-referenceblob.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o" -o ../../../test-bin/test-referenceblob -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a -[ 97%] Linking C executable ../../../bin/fastconv +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-sql\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-sql/CMakeFiles/fastconv.dir/fastconv.c.o -MF CMakeFiles/fastconv.dir/fastconv.c.o.d -o CMakeFiles/fastconv.dir/fastconv.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql/fastconv.c +[ 98%] Linking CXX executable ../../../test-bin/test-ngs-vdb +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs-vdb.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o" -o ../../../test-bin/test-ngs-vdb ../../../ilib/libtk-version.a ../../../ilib/libngs-vdb.a -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target test-ngs_sradb_c++ +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target test-ngs-vdb +[ 98%] Linking C executable ../../../bin/fastconv cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastconv.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/fastconv.dir/fastconv.c.o -o ../../../bin/fastconv /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a ../../../ilib/libvdb-sqlite.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target test-referenceblob -[ 97%] Linking CXX executable ../../../test-bin/test-ngs_sradb -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sradb.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o" -o ../../../test-bin/test-ngs_sradb -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastconv.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fastconv fastconv.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastconv.3.0.3 fastconv.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastconv.3 fastconv make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target fastconv -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target test-ngs_sradb -[ 97%] Linking CXX executable ../../../test-bin/test-ngs_sradb_c++ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sradb_c++.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o" -o ../../../test-bin/test-ngs_sradb_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target test-ngs_sradb_c++ -[ 98%] Linking CXX executable ../../../test-bin/test-ngs_sra -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sra.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o" -o ../../../test-bin/test-ngs_sra -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target test-ngs_sra +[ 98%] Built target fastconv [ 98%] Linking C executable ../../../bin/vdb-sql cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-sql.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-sql.dir/vdb_shell.c.o" -o ../../../bin/vdb-sql ../../../ilib/libvdb-sqlite.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a -[ 98%] Linking CXX executable ../../../test-bin/test-ngs_csra1 -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o" -o ../../../test-bin/test-ngs_csra1 -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-sql.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-sql vdb-sql.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-sql.3.0.3 vdb-sql.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-sql.3 vdb-sql make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target vdb-sql -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target test-ngs_csra1 -[ 98%] Linking CXX executable ../../../test-bin/test-ngs-vdb -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs-vdb.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o" -o ../../../test-bin/test-ngs-vdb ../../../ilib/libtk-version.a ../../../ilib/libngs-vdb.a -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target test-ngs-vdb In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./taskflow/core/../utility/traits.hpp:29, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./taskflow/core/graph.hpp:5, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./taskflow/core/task.hpp:3, @@ -7638,11 +7674,6 @@ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:1892:25: note: '*(unsigned char*)((char*)&opt_pcr_dup + offsetof(std::optional,std::optional::.std::_Optional_base::))' was declared here 1892 | std::optional opt_pcr_dup; | ^~~~~~~~~~~ -[ 98%] Linking CXX executable ../../../test-bin/test-ngs_csra1_c++ -cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_c++.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o" -o ../../../test-bin/test-ngs_csra1_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a -make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target test-ngs_csra1_c++ [ 98%] Linking CXX executable ../../../bin/bam-load cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam-load.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/bam-load.dir/bam-loader.c.o" "CMakeFiles/bam-load.dir/bam.c.o" "CMakeFiles/bam-load.dir/sam.c.o" "CMakeFiles/bam-load.dir/alignment-writer.c.o" "CMakeFiles/bam-load.dir/reference-writer.c.o" "CMakeFiles/bam-load.dir/sequence-writer.c.o" "CMakeFiles/bam-load.dir/loader-imp.c.o" "CMakeFiles/bam-load.dir/mem-bank.cpp.o" "CMakeFiles/bam-load.dir/low-match-count.cpp.o" -o ../../../bin/bam-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -lz /usr/lib/x86_64-linux-gnu/libcrypto.so @@ -7652,6 +7683,11 @@ cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s bam-load.3 bam-load make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target bam-load +[ 98%] Linking CXX executable ../../../test-bin/test-ngs_csra1_c++ +cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_c++.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o" -o ../../../test-bin/test-ngs_csra1_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a +make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target test-ngs_csra1_c++ [ 99%] Linking CXX executable ../../../bin/sharq cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq && /usr/bin/cmake -E cmake_link_script CMakeFiles/sharq.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/sharq.dir/fastq_parse.cpp.o -o ../../../bin/sharq -lstdc++fs /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libbz2.so -lre2 @@ -7668,10 +7704,10 @@ make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' +make -f test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/build make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' -make -f test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/build +make -f test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 99%] Building CXX object test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/test-sharq-parser.cpp.o [ 99%] Building CXX object test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/test-sharq-writer.cpp.o @@ -7734,7 +7770,7 @@ 9: Test timeout computed to be: 1500 9: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-python/setup.py:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives 9: from distutils.core import setup - 1/114 Test #9: Test_NGS_Python_install ......................... Passed 0.50 sec + 1/114 Test #9: Test_NGS_Python_install ......................... Passed 0.87 sec test 15 Start 15: Ngs_MakeDB @@ -7745,7 +7781,7 @@ 15: SparseFragmentBlobs (0 s) 15: 15: *** No errors detected (0 s total) - 2/114 Test #15: Ngs_MakeDB ...................................... Passed 0.15 sec + 2/114 Test #15: Ngs_MakeDB ...................................... Passed 0.41 sec test 16 Start 16: Test_Ngs @@ -7754,7 +7790,7 @@ 16: Test timeout computed to be: 1500 16: 16: *** No errors detected (0 s total) - 3/114 Test #16: Test_Ngs ........................................ Passed 0.03 sec + 3/114 Test #16: Test_Ngs ........................................ Passed 0.06 sec test 32 Start 32: GeneralWriterTest @@ -7786,25 +7822,25 @@ 32: addTable correctly failed 32: endStream Success 32: --------------------------------- - 4/114 Test #32: GeneralWriterTest ............................... Passed 0.02 sec + 4/114 Test #32: GeneralWriterTest ............................... Passed 0.04 sec test 33 Start 33: Ref-Variation-1.0 33: Test command: /bin/sh "./have-access.sh" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "ref-variation" 33: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/test 33: Test timeout computed to be: 1500 -33: ./have-access.sh: 6: vdb-config: not found +33: ./have-access.sh: line 6: vdb-config: command not found 33: no access to repository, skipping ref-variation test... - 5/114 Test #33: Ref-Variation-1.0 ............................... Passed 0.02 sec + 5/114 Test #33: Ref-Variation-1.0 ............................... Passed 0.04 sec test 34 Start 34: Var-Expand-1.0 34: Test command: /bin/sh "./have-access.sh" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "var-expand" 34: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/test 34: Test timeout computed to be: 1500 -34: ./have-access.sh: 6: vdb-config: not found +34: ./have-access.sh: line 6: vdb-config: command not found 34: no access to repository, skipping var-expand test... - 6/114 Test #34: Var-Expand-1.0 .................................. Passed 0.01 sec + 6/114 Test #34: Var-Expand-1.0 .................................. Passed 0.04 sec test 35 Start 35: SearchBlockWhiteBox @@ -7822,7 +7858,7 @@ 35: SearchSmithWaterman_Coords_NotSupported (0 s) 35: 35: *** No errors detected (0 s total) - 7/114 Test #35: SearchBlockWhiteBox ............................. Passed 0.03 sec + 7/114 Test #35: SearchBlockWhiteBox ............................. Passed 0.04 sec test 38 Start 38: GeneralLoaderWhiteBox @@ -7893,7 +7929,7 @@ 38: ProgressMessage (0 s) 38: TargetOverride (0 s) 38: -38: *** No errors detected (0 s total) +38: *** No errors detected (1 s total) 38: Packed protocol: Running 62 test cases... 38: EmptyInput (0 s) 38: ShortInput (0 s) @@ -7959,21 +7995,21 @@ 38: TargetOverride (0 s) 38: 38: *** No errors detected (1 s total) - 8/114 Test #38: GeneralLoaderWhiteBox ........................... Passed 2.19 sec + 8/114 Test #38: GeneralLoaderWhiteBox ........................... Passed 3.42 sec test 39 Start 39: GWDumper 39: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-gw-dumper 39: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test 39: Test timeout computed to be: 1500 - 9/114 Test #39: GWDumper ........................................ Passed 0.02 sec + 9/114 Test #39: GWDumper ........................................ Passed 0.07 sec test 40 Start 40: makeinputs 40: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/makeinputs 40: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 40: Test timeout computed to be: 1500 - 10/114 Test #40: makeinputs ...................................... Passed 0.04 sec + 10/114 Test #40: makeinputs ...................................... Passed 0.07 sec test 41 Start 41: GeneralLoader-1.0-Basic-Unpacked @@ -7985,7 +8021,7 @@ 41: cat input/1.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/load.stderr 41: Load succeeded, dumping and matching stdout 41: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/dump.stderr - 11/114 Test #41: GeneralLoader-1.0-Basic-Unpacked ................ Passed 0.65 sec + 11/114 Test #41: GeneralLoader-1.0-Basic-Unpacked ................ Passed 1.37 sec test 42 Start 42: GeneralLoader-1.1-Basic-Packed @@ -7997,7 +8033,7 @@ 42: cat input/1packed.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/load.stderr 42: Load succeeded, dumping and matching stdout 42: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/dump.stderr - 12/114 Test #42: GeneralLoader-1.1-Basic-Packed .................. Passed 0.60 sec + 12/114 Test #42: GeneralLoader-1.1-Basic-Packed .................. Passed 1.27 sec test 43 Start 43: GeneralLoader-1.2-TargetDbOverride @@ -8009,7 +8045,7 @@ 43: cat input/1override.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb --target actual/1override/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stderr 43: Load succeeded, dumping and matching stdout 43: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stderr - 13/114 Test #43: GeneralLoader-1.2-TargetDbOverride .............. Passed 0.60 sec + 13/114 Test #43: GeneralLoader-1.2-TargetDbOverride .............. Passed 1.29 sec test 44 Start 44: GeneralLoader-1.3-TargetDbOverrideShorthand @@ -8021,7 +8057,7 @@ 44: cat input/1override.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -T actual/1override/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stderr 44: Load succeeded, dumping and matching stdout 44: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stderr - 14/114 Test #44: GeneralLoader-1.3-TargetDbOverrideShorthand ..... Passed 0.56 sec + 14/114 Test #44: GeneralLoader-1.3-TargetDbOverrideShorthand ..... Passed 1.20 sec test 45 Start 45: GeneralLoader-2.0-ErrorMessageEvent-Unpacked @@ -8032,7 +8068,7 @@ 45: running test case 2 45: cat input/2.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -L=err 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2/load.stderr 45: Load failed as expected, matching stderr - 15/114 Test #45: GeneralLoader-2.0-ErrorMessageEvent-Unpacked .... Passed 0.36 sec + 15/114 Test #45: GeneralLoader-2.0-ErrorMessageEvent-Unpacked .... Passed 0.79 sec test 46 Start 46: GeneralLoader-2.1-ErrorMessageEvent-Packed @@ -8043,7 +8079,7 @@ 46: running test case 2packed 46: cat input/2packed.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -L=err 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2packed/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2packed/load.stderr 46: Load failed as expected, matching stderr - 16/114 Test #46: GeneralLoader-2.1-ErrorMessageEvent-Packed ...... Passed 0.39 sec + 16/114 Test #46: GeneralLoader-2.1-ErrorMessageEvent-Packed ...... Passed 0.84 sec test 47 Start 47: GeneralLoader-3.0-EmptyDefaultValues-Unpacked @@ -8055,7 +8091,7 @@ 47: cat input/3.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stderr 47: Load succeeded, dumping and matching stdout 47: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stderr - 17/114 Test #47: GeneralLoader-3.0-EmptyDefaultValues-Unpacked ... Passed 0.53 sec + 17/114 Test #47: GeneralLoader-3.0-EmptyDefaultValues-Unpacked ... Passed 1.37 sec test 48 Start 48: GeneralLoader-3.1-EmptyDefaultValues-Packed @@ -8067,7 +8103,7 @@ 48: cat input/3.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stderr 48: Load succeeded, dumping and matching stdout 48: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stderr - 18/114 Test #48: GeneralLoader-3.1-EmptyDefaultValues-Packed ..... Passed 0.52 sec + 18/114 Test #48: GeneralLoader-3.1-EmptyDefaultValues-Packed ..... Passed 1.27 sec test 49 Start 49: GeneralLoader-4.0-MoveAheadEvent-Unpacked @@ -8079,7 +8115,7 @@ 49: cat input/4.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/load.stderr 49: Load succeeded, dumping and matching stdout 49: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/dump.stderr - 19/114 Test #49: GeneralLoader-4.0-MoveAheadEvent-Unpacked ....... Passed 0.57 sec + 19/114 Test #49: GeneralLoader-4.0-MoveAheadEvent-Unpacked ....... Passed 1.09 sec test 50 Start 50: GeneralLoader-4.1-MoveAheadEvent-Packed @@ -8091,7 +8127,7 @@ 50: cat input/4packed.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/load.stderr 50: Load succeeded, dumping and matching stdout 50: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/dump.stderr - 20/114 Test #50: GeneralLoader-4.1-MoveAheadEvent-Packed ......... Passed 0.47 sec + 20/114 Test #50: GeneralLoader-4.1-MoveAheadEvent-Packed ......... Passed 1.28 sec test 51 Start 51: GeneralLoader-5.0-IntegerConversion @@ -8103,7 +8139,7 @@ 51: cat input/5packed.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/load.stderr 51: Load succeeded, dumping and matching stdout 51: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/dump.stderr - 21/114 Test #51: GeneralLoader-5.0-IntegerConversion ............. Passed 0.54 sec + 21/114 Test #51: GeneralLoader-5.0-IntegerConversion ............. Passed 1.09 sec test 52 Start 52: GeneralLoader-6.0-SoftwareName-Unpacked @@ -8115,7 +8151,7 @@ 52: cat input/6.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -L=info -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/load.stderr 52: Load succeeded, dumping and matching stdout 52: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/db SOFTWARE/formatter 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/dump.stderr - 22/114 Test #52: GeneralLoader-6.0-SoftwareName-Unpacked ......... Passed 0.40 sec + 22/114 Test #52: GeneralLoader-6.0-SoftwareName-Unpacked ......... Passed 1.00 sec test 53 Start 53: GeneralLoader-6.1-SoftwareName-Packed @@ -8127,14 +8163,14 @@ 53: cat input/6packed.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -L=info -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/load.stderr 53: Load succeeded, dumping and matching stdout 53: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/db SOFTWARE/formatter 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/dump.stderr - 23/114 Test #53: GeneralLoader-6.1-SoftwareName-Packed ........... Passed 0.20 sec + 23/114 Test #53: GeneralLoader-6.1-SoftwareName-Packed ........... Passed 1.20 sec test 54 Start 54: bio-end-makeinputs 54: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/bio-end-makeinputs 54: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 54: Test timeout computed to be: 1500 - 24/114 Test #54: bio-end-makeinputs .............................. Passed 0.01 sec + 24/114 Test #54: bio-end-makeinputs .............................. Passed 0.06 sec test 55 Start 55: BioEnd-Excl-1 @@ -8142,7 +8178,7 @@ 55: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 55: Test timeout computed to be: 1500 55: running test bio-end:excl-1 - 25/114 Test #55: BioEnd-Excl-1 ................................... Passed 0.48 sec + 25/114 Test #55: BioEnd-Excl-1 ................................... Passed 0.77 sec test 56 Start 56: BioEnd-Excl-2 @@ -8150,7 +8186,7 @@ 56: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 56: Test timeout computed to be: 1500 56: running test bio-end:excl-2 - 26/114 Test #56: BioEnd-Excl-2 ................................... Passed 0.48 sec + 26/114 Test #56: BioEnd-Excl-2 ................................... Passed 0.90 sec test 57 Start 57: BioEnd-Excl-3 @@ -8158,7 +8194,7 @@ 57: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 57: Test timeout computed to be: 1500 57: running test bio-end:excl-3 - 27/114 Test #57: BioEnd-Excl-3 ................................... Passed 0.48 sec + 27/114 Test #57: BioEnd-Excl-3 ................................... Passed 1.07 sec test 58 Start 58: BioEnd-Excl-4 @@ -8166,7 +8202,7 @@ 58: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 58: Test timeout computed to be: 1500 58: running test bio-end:excl-4 - 28/114 Test #58: BioEnd-Excl-4 ................................... Passed 0.43 sec + 28/114 Test #58: BioEnd-Excl-4 ................................... Passed 0.97 sec test 59 Start 59: BioEnd-Incl-1 @@ -8174,7 +8210,7 @@ 59: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 59: Test timeout computed to be: 1500 59: running test bio-end:incl-1 - 29/114 Test #59: BioEnd-Incl-1 ................................... Passed 0.49 sec + 29/114 Test #59: BioEnd-Incl-1 ................................... Passed 0.98 sec test 60 Start 60: IdxText-CI-1 @@ -8182,14 +8218,14 @@ 60: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 60: Test timeout computed to be: 1500 60: running test bio-end:excl-1 - 30/114 Test #60: IdxText-CI-1 .................................... Passed 0.36 sec + 30/114 Test #60: IdxText-CI-1 .................................... Passed 0.76 sec test 61 Start 61: idx-text-makeinputs 61: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-makeinputs 61: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 61: Test timeout computed to be: 1500 - 31/114 Test #61: idx-text-makeinputs ............................. Passed 0.01 sec + 31/114 Test #61: idx-text-makeinputs ............................. Passed 0.07 sec test 62 Start 62: IdxText-ci-1 @@ -8197,7 +8233,7 @@ 62: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 62: Test timeout computed to be: 1500 62: running test idx-text:ci-1 - 32/114 Test #62: IdxText-ci-1 .................................... Passed 0.54 sec + 32/114 Test #62: IdxText-ci-1 .................................... Passed 1.14 sec test 63 Start 63: IdxText-ci-2 @@ -8205,7 +8241,7 @@ 63: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 63: Test timeout computed to be: 1500 63: running test idx-text:ci-2 - 33/114 Test #63: IdxText-ci-2 .................................... Passed 0.50 sec + 33/114 Test #63: IdxText-ci-2 .................................... Passed 0.91 sec test 64 Start 64: IdxText-ci-3 @@ -8213,7 +8249,7 @@ 64: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 64: Test timeout computed to be: 1500 64: running test idx-text:ci-3 - 34/114 Test #64: IdxText-ci-3 .................................... Passed 0.59 sec + 34/114 Test #64: IdxText-ci-3 .................................... Passed 0.64 sec test 65 Start 65: IdxText-ci-4 @@ -8221,7 +8257,7 @@ 65: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 65: Test timeout computed to be: 1500 65: running test idx-text:ci-4 - 35/114 Test #65: IdxText-ci-4 .................................... Passed 0.48 sec + 35/114 Test #65: IdxText-ci-4 .................................... Passed 1.15 sec test 66 Start 66: IdxText-ci-5 @@ -8229,7 +8265,7 @@ 66: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 66: Test timeout computed to be: 1500 66: running test idx-text:ci-5 - 36/114 Test #66: IdxText-ci-5 .................................... Passed 0.33 sec + 36/114 Test #66: IdxText-ci-5 .................................... Passed 0.81 sec test 67 Start 67: IdxText-cs-1 @@ -8237,7 +8273,7 @@ 67: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 67: Test timeout computed to be: 1500 67: running test idx-text:cs-1 - 37/114 Test #67: IdxText-cs-1 .................................... Passed 0.56 sec + 37/114 Test #67: IdxText-cs-1 .................................... Passed 0.96 sec test 68 Start 68: IdxText-cs-2 @@ -8245,7 +8281,7 @@ 68: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 68: Test timeout computed to be: 1500 68: running test idx-text:cs-2 - 38/114 Test #68: IdxText-cs-2 .................................... Passed 0.59 sec + 38/114 Test #68: IdxText-cs-2 .................................... Passed 1.04 sec test 69 Start 69: IdxText-cs-3 @@ -8253,7 +8289,7 @@ 69: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 69: Test timeout computed to be: 1500 69: running test idx-text:cs-3 - 39/114 Test #69: IdxText-cs-3 .................................... Passed 0.43 sec + 39/114 Test #69: IdxText-cs-3 .................................... Passed 0.69 sec test 70 Start 70: PileupStats-Version @@ -8261,14 +8297,14 @@ grep --quiet `head -n 1 /build/sra-sdk-3.0.3+dfsg/shared/toolkit.vers`" 70: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 70: Test timeout computed to be: 1500 - 40/114 Test #70: PileupStats-Version ............................. Passed 0.06 sec + 40/114 Test #70: PileupStats-Version ............................. Passed 0.07 sec test 71 Start 71: PileupStats-Help 71: Test command: /bin/sh "-c" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -h | grep --quiet Usage" 71: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 71: Test timeout computed to be: 1500 - 41/114 Test #71: PileupStats-Help ................................ Passed 0.05 sec + 41/114 Test #71: PileupStats-Help ................................ Passed 0.06 sec test 72 Start 72: PileupStats-NoArgs @@ -8299,8 +8335,7 @@ 72: 72: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 72: -72: /bin/sh: 1: [: 3: unexpected operator - 42/114 Test #72: PileupStats-NoArgs .............................. Passed 0.02 sec + 42/114 Test #72: PileupStats-NoArgs .............................. Passed 0.06 sec test 73 Start 73: PileupStats-IgnoreArgs-L @@ -8331,8 +8366,7 @@ 73: 73: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 73: -73: /bin/sh: 1: [: 3: unexpected operator - 43/114 Test #73: PileupStats-IgnoreArgs-L ........................ Passed 0.05 sec + 43/114 Test #73: PileupStats-IgnoreArgs-L ........................ Passed 0.08 sec test 74 Start 74: PileupStats-IgnoreArgs-z @@ -8363,8 +8397,7 @@ 74: 74: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 74: -74: /bin/sh: 1: [: 3: unexpected operator - 44/114 Test #74: PileupStats-IgnoreArgs-z ........................ Passed 0.02 sec + 44/114 Test #74: PileupStats-IgnoreArgs-z ........................ Passed 0.08 sec test 75 Start 75: PileupStats-IgnoreArgs-loglevel @@ -8395,8 +8428,7 @@ 75: 75: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 75: -75: /bin/sh: 1: [: 3: unexpected operator - 45/114 Test #75: PileupStats-IgnoreArgs-loglevel ................. Passed 0.03 sec + 45/114 Test #75: PileupStats-IgnoreArgs-loglevel ................. Passed 0.08 sec test 76 Start 76: PileupStats-IgnoreArgs-xmllog @@ -8427,8 +8459,7 @@ 76: 76: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 76: -76: /bin/sh: 1: [: 3: unexpected operator - 46/114 Test #76: PileupStats-IgnoreArgs-xmllog ................... Passed 0.05 sec + 46/114 Test #76: PileupStats-IgnoreArgs-xmllog ................... Passed 0.07 sec test 77 Start 77: PileupStats-IgnoreArgs-xmllogfd @@ -8459,8 +8490,7 @@ 77: 77: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 77: -77: /bin/sh: 1: [: 3: unexpected operator - 47/114 Test #77: PileupStats-IgnoreArgs-xmllogfd ................. Passed 0.04 sec + 47/114 Test #77: PileupStats-IgnoreArgs-xmllogfd ................. Passed 0.06 sec test 78 Start 78: Test_NgsJava_lib_load @@ -8469,11 +8499,11 @@ 78: Test timeout computed to be: 1500 78: JUnit version 4.11 78: ......... -78: Time: 0.337 +78: Time: 0.681 78: 78: OK (9 tests) 78: - 48/114 Test #78: Test_NgsJava_lib_load ........................... Passed 1.22 sec + 48/114 Test #78: Test_NgsJava_lib_load ........................... Passed 3.70 sec test 82 Start 82: Test_Drivertool_BuildVersion @@ -8481,7 +8511,7 @@ 82: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 82: Test timeout computed to be: 1500 82: Test_Version passed. - 49/114 Test #82: Test_Drivertool_BuildVersion .................... Passed 0.02 sec + 49/114 Test #82: Test_Drivertool_BuildVersion .................... Passed 0.05 sec test 83 Start 83: Test_Drivertool_FilePath @@ -8517,7 +8547,7 @@ 83: Executable_Yes (0 s) 83: 83: *** No errors detected (0 s total) - 50/114 Test #83: Test_Drivertool_FilePath ........................ Passed 0.03 sec + 50/114 Test #83: Test_Drivertool_FilePath ........................ Passed 0.05 sec test 84 Start 84: Test_Drivertool_CommandLine @@ -8525,35 +8555,35 @@ 84: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 84: Test timeout computed to be: 1500 84: Test_CommandLine passed. - 51/114 Test #84: Test_Drivertool_CommandLine ..................... Passed 0.02 sec + 51/114 Test #84: Test_Drivertool_CommandLine ..................... Passed 0.06 sec test 85 Start 85: Test_Drivertool_JsonParsing 85: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_JsonParsing 85: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 85: Test timeout computed to be: 1500 - 52/114 Test #85: Test_Drivertool_JsonParsing ..................... Passed 0.05 sec + 52/114 Test #85: Test_Drivertool_JsonParsing ..................... Passed 0.10 sec test 86 Start 86: Test_Drivertool_SDLResponse 86: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_SDLResponse 86: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 86: Test timeout computed to be: 1500 - 53/114 Test #86: Test_Drivertool_SDLResponse ..................... Passed 0.02 sec + 53/114 Test #86: Test_Drivertool_SDLResponse ..................... Passed 0.04 sec test 87 Start 87: Test_Drivertool_Accession 87: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_Accession 87: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 87: Test timeout computed to be: 1500 - 54/114 Test #87: Test_Drivertool_Accession ....................... Passed 0.02 sec + 54/114 Test #87: Test_Drivertool_Accession ....................... Passed 0.03 sec test 88 Start 88: Test_Drivertool_UUID 88: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_UUID 88: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 88: Test timeout computed to be: 1500 - 55/114 Test #88: Test_Drivertool_UUID ............................ Passed 2.07 sec + 55/114 Test #88: Test_Drivertool_UUID ............................ Passed 4.43 sec test 90 Start 90: Test_VDB_Config_model @@ -8576,7 +8606,7 @@ 90: 90: *** No errors detected (0 s total) 90: VDB Copy model test is finished - 56/114 Test #90: Test_VDB_Config_model ........................... Passed 0.25 sec + 56/114 Test #90: Test_VDB_Config_model ........................... Passed 0.38 sec test 91 Start 91: Test_Vdb_dump_Check_exit_code @@ -8585,7 +8615,7 @@ 91: Test timeout computed to be: 1500 91: WARNING[TEST1] help message is in 'STDOUT' 91: [check-exit-code.py] test passed for [/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump] - 57/114 Test #91: Test_Vdb_dump_Check_exit_code ................... Passed 0.38 sec + 57/114 Test #91: Test_Vdb_dump_Check_exit_code ................... Passed 0.75 sec test 93 Start 93: Test_KAPP_qfile @@ -8596,7 +8626,7 @@ 93: queue-size : 1024 93: block-size : 0 93: chunk-size : 1024 - 58/114 Test #93: Test_KAPP_qfile ................................. Passed 0.02 sec + 58/114 Test #93: Test_KAPP_qfile ................................. Passed 0.06 sec test 94 Start 94: Test_LOADERFILE @@ -8611,7 +8641,7 @@ 94: KLoaderFile_noEolBeforeEof (0 s) 94: 94: *** No errors detected (7 s total) - 59/114 Test #94: Test_LOADERFILE ................................. Passed 7.13 sec + 59/114 Test #94: Test_LOADERFILE ................................. Passed 7.12 sec test 95 Start 95: Test_LOADER @@ -8623,7 +8653,7 @@ 95: LoaderMeta_WriteWithVersion (0 s) 95: 95: *** No errors detected (0 s total) - 60/114 Test #95: Test_LOADER ..................................... Passed 0.17 sec + 60/114 Test #95: Test_LOADER ..................................... Passed 0.27 sec test 96 Start 96: Test_regexpr @@ -8637,7 +8667,7 @@ 96: YesMatch (0 s) 96: 96: *** No errors detected (0 s total) - 61/114 Test #96: Test_regexpr .................................... Passed 0.03 sec + 61/114 Test #96: Test_regexpr .................................... Passed 0.06 sec test 97 Start 97: Test_sharq_parser @@ -8717,11 +8747,11 @@ 97: Quality33Adjusteed (0 s) 97: Quality64TooLow (0 s) 97: Quality64Adjusted (0 s) -97: [2024-08-24 00:18:05.546] [warning] [code:130] Read DG7PMJN1:293:D12THACXX:2:1101:1161:1968: quality score length exceeds sequence length +97: [2023-07-23 20:32:56.964] [warning] [code:130] Read DG7PMJN1:293:D12THACXX:2:1101:1161:1968: quality score length exceeds sequence length 97: TextQualityTruncated (0 s) 97: TextQualityAccepted (0 s) 97: TextQualityAdjusted (0 s) -97: [2024-08-24 00:18:05.554] [warning] [code:130] Read DG7PMJN1:293:D12THACXX:2:1101:1161:1968: quality score length exceeds sequence length +97: [2023-07-23 20:32:56.985] [warning] [code:130] Read DG7PMJN1:293:D12THACXX:2:1101:1161:1968: quality score length exceeds sequence length 97: QualityTooLongTruncated (0 s) 97: Nanopore1_readno_early (0 s) 97: Nanopore1_readno_late (0 s) @@ -8741,8 +8771,8 @@ 97: Nanopore_Barcode_BC (0 s) 97: Nanopore_Barcode_Edit (0 s) 97: -97: *** No errors detected (0 s total) - 62/114 Test #97: Test_sharq_parser ............................... Passed 0.37 sec +97: *** No errors detected (1 s total) + 62/114 Test #97: Test_sharq_parser ............................... Passed 1.24 sec test 98 Start 98: Test_sharq_writer @@ -8759,7 +8789,7 @@ 98: NanoporeSpecificColumns (0 s) 98: 98: *** No errors detected (0 s total) - 63/114 Test #98: Test_sharq_writer ............................... Passed 0.01 sec + 63/114 Test #98: Test_sharq_writer ............................... Passed 0.04 sec test 99 Start 99: Test_001.read.supported @@ -8768,7 +8798,7 @@ 99: Test timeout computed to be: 1500 99: running 001.read.supported 99: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/001.R1.fastq 1>./actual/001.read.supported/load.stdout 2>./actual/001.read.supported/load.stderr - 64/114 Test #99: Test_001.read.supported ......................... Passed 0.12 sec + 64/114 Test #99: Test_001.read.supported ......................... Passed 0.25 sec test 100 Start 100: Test_001.read.unsupported @@ -8777,7 +8807,7 @@ 100: Test timeout computed to be: 1500 100: running 001.read.unsupported 100: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.unsupported.fq 1>./actual/001.read.unsupported/load.stdout 2>./actual/001.read.unsupported/load.stderr - 65/114 Test #100: Test_001.read.unsupported ....................... Passed 0.05 sec + 65/114 Test #100: Test_001.read.unsupported ....................... Passed 0.19 sec test 101 Start 101: Test_001.read.no_sequence @@ -8786,7 +8816,7 @@ 101: Test timeout computed to be: 1500 101: running 001.read.no_sequence 101: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.no_sequence.fq 1>./actual/001.read.no_sequence/load.stdout 2>./actual/001.read.no_sequence/load.stderr - 66/114 Test #101: Test_001.read.no_sequence ....................... Passed 0.05 sec + 66/114 Test #101: Test_001.read.no_sequence ....................... Passed 0.19 sec test 102 Start 102: Test_001.read.invalid_sequence @@ -8795,7 +8825,7 @@ 102: Test timeout computed to be: 1500 102: running 001.read.invalid_sequence 102: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.invalid_sequence.fq 1>./actual/001.read.invalid_sequence/load.stdout 2>./actual/001.read.invalid_sequence/load.stderr - 67/114 Test #102: Test_001.read.invalid_sequence .................. Passed 0.03 sec + 67/114 Test #102: Test_001.read.invalid_sequence .................. Passed 0.33 sec test 103 Start 103: Test_001.read.no_quality @@ -8804,7 +8834,7 @@ 103: Test timeout computed to be: 1500 103: running 001.read.no_quality 103: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.no_quality.fq 1>./actual/001.read.no_quality/load.stdout 2>./actual/001.read.no_quality/load.stderr - 68/114 Test #103: Test_001.read.no_quality ........................ Passed 0.11 sec + 68/114 Test #103: Test_001.read.no_quality ........................ Passed 0.24 sec test 104 Start 104: Test_001.read.no_quality_2 @@ -8813,7 +8843,7 @@ 104: Test timeout computed to be: 1500 104: running 001.read.no_quality_2 104: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.no_quality_2.fq 1>./actual/001.read.no_quality_2/load.stdout 2>./actual/001.read.no_quality_2/load.stderr - 69/114 Test #104: Test_001.read.no_quality_2 ...................... Passed 0.12 sec + 69/114 Test #104: Test_001.read.no_quality_2 ...................... Passed 0.30 sec test 105 Start 105: Test_001.read.invalid_quality33 @@ -8822,7 +8852,7 @@ 105: Test timeout computed to be: 1500 105: running 001.read.invalid_quality33 105: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --quality=33 input/001.read.invalid_quality33.fq 1>./actual/001.read.invalid_quality33/load.stdout 2>./actual/001.read.invalid_quality33/load.stderr - 70/114 Test #105: Test_001.read.invalid_quality33 ................. Passed 0.13 sec + 70/114 Test #105: Test_001.read.invalid_quality33 ................. Passed 0.15 sec test 106 Start 106: Test_001.read.invalid_quality64 @@ -8831,7 +8861,7 @@ 106: Test timeout computed to be: 1500 106: running 001.read.invalid_quality64 106: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --quality=64 input/001.read.invalid_quality64.fq 1>./actual/001.read.invalid_quality64/load.stdout 2>./actual/001.read.invalid_quality64/load.stderr - 71/114 Test #106: Test_001.read.invalid_quality64 ................. Passed 0.12 sec + 71/114 Test #106: Test_001.read.invalid_quality64 ................. Passed 0.13 sec test 107 Start 107: Test_001.read.invalid_quality0 @@ -8840,7 +8870,7 @@ 107: Test timeout computed to be: 1500 107: running 001.read.invalid_quality0 107: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --quality=0 input/001.read.invalid_quality0.fq 1>./actual/001.read.invalid_quality0/load.stdout 2>./actual/001.read.invalid_quality0/load.stderr - 72/114 Test #107: Test_001.read.invalid_quality0 .................. Passed 0.11 sec + 72/114 Test #107: Test_001.read.invalid_quality0 .................. Passed 0.12 sec test 108 Start 108: Test_001.read.long_quality @@ -8849,7 +8879,7 @@ 108: Test timeout computed to be: 1500 108: running 001.read.long_quality 108: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.long_quality.fq 1>./actual/001.read.long_quality/load.stdout 2>./actual/001.read.long_quality/load.stderr - 73/114 Test #108: Test_001.read.long_quality ...................... Passed 0.14 sec + 73/114 Test #108: Test_001.read.long_quality ...................... Passed 0.20 sec test 109 Start 109: Test_001.read.bad_quality0 @@ -8858,7 +8888,7 @@ 109: Test timeout computed to be: 1500 109: running 001.read.bad_quality0 109: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.bad_quality0.fq 1>./actual/001.read.bad_quality0/load.stdout 2>./actual/001.read.bad_quality0/load.stderr - 74/114 Test #109: Test_001.read.bad_quality0 ...................... Passed 0.12 sec + 74/114 Test #109: Test_001.read.bad_quality0 ...................... Passed 0.14 sec test 110 Start 110: Test_001.read.bad_quality33 @@ -8876,7 +8906,7 @@ 111: Test timeout computed to be: 1500 111: running 002.readTypes_default 111: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/002.allBiological_1.fq input/002.allBiological_2.fq 1>./actual/002.readTypes_default/load.stdout 2>./actual/002.readTypes_default/load.stderr - 76/114 Test #111: Test_002.readTypes_default ...................... Passed 0.17 sec + 76/114 Test #111: Test_002.readTypes_default ...................... Passed 0.25 sec test 112 Start 112: Test_002.readTypes_technical @@ -8885,7 +8915,7 @@ 112: Test timeout computed to be: 1500 112: running 002.readTypes_technical 112: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=TT input/002.allBiological_1.fq input/002.allBiological_2.fq 1>./actual/002.readTypes_technical/load.stdout 2>./actual/002.readTypes_technical/load.stderr - 77/114 Test #112: Test_002.readTypes_technical .................... Passed 0.16 sec + 77/114 Test #112: Test_002.readTypes_technical .................... Passed 0.33 sec test 113 Start 113: Test_002.readTypes_mixed @@ -8894,7 +8924,7 @@ 113: Test timeout computed to be: 1500 113: running 002.readTypes_mixed 113: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=TB input/002.allBiological_1.fq input/002.allBiological_2.fq 1>./actual/002.readTypes_mixed/load.stdout 2>./actual/002.readTypes_mixed/load.stderr - 78/114 Test #113: Test_002.readTypes_mixed ........................ Passed 0.19 sec + 78/114 Test #113: Test_002.readTypes_mixed ........................ Passed 0.29 sec test 114 Start 114: Test_002.readTypes_missing @@ -8903,7 +8933,7 @@ 114: Test timeout computed to be: 1500 114: running 002.readTypes_missing 114: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --read1PairFiles=input/001.R1.fastq 1>./actual/002.readTypes_missing/load.stdout 2>./actual/002.readTypes_missing/load.stderr - 79/114 Test #114: Test_002.readTypes_missing ...................... Passed 0.11 sec + 79/114 Test #114: Test_002.readTypes_missing ...................... Passed 0.12 sec test 115 Start 115: Test_002.readTypes_mismatch @@ -8912,7 +8942,7 @@ 115: Test timeout computed to be: 1500 115: running 002.readTypes_mismatch 115: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=TB --read1PairFiles=input/001.R1.fastq 1>./actual/002.readTypes_mismatch/load.stdout 2>./actual/002.readTypes_mismatch/load.stderr - 80/114 Test #115: Test_002.readTypes_mismatch ..................... Passed 0.13 sec + 80/114 Test #115: Test_002.readTypes_mismatch ..................... Passed 0.14 sec test 116 Start 116: Test_002.readTypes_unexpected @@ -8921,7 +8951,7 @@ 116: Test timeout computed to be: 1500 116: running 002.readTypes_unexpected 116: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=X --read1PairFiles=input/002.allBiological_1.fq 1>./actual/002.readTypes_unexpected/load.stdout 2>./actual/002.readTypes_unexpected/load.stderr - 81/114 Test #116: Test_002.readTypes_unexpected ................... Passed 0.11 sec + 81/114 Test #116: Test_002.readTypes_unexpected ................... Passed 0.20 sec test 117 Start 117: Test_002.readTypes_interlaved_fail_1 @@ -8930,7 +8960,7 @@ 117: Test timeout computed to be: 1500 117: running 002.readTypes_interlaved_fail_1 117: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq 1>./actual/002.readTypes_interlaved_fail_1/load.stdout 2>./actual/002.readTypes_interlaved_fail_1/load.stderr - 82/114 Test #117: Test_002.readTypes_interlaved_fail_1 ............ Passed 0.07 sec + 82/114 Test #117: Test_002.readTypes_interlaved_fail_1 ............ Passed 0.39 sec test 118 Start 118: Test_002.readTypes_interlaved_fail_2 @@ -8939,7 +8969,7 @@ 118: Test timeout computed to be: 1500 118: running 002.readTypes_interlaved_fail_2 118: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BB input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq 1>./actual/002.readTypes_interlaved_fail_2/load.stdout 2>./actual/002.readTypes_interlaved_fail_2/load.stderr - 83/114 Test #118: Test_002.readTypes_interlaved_fail_2 ............ Passed 0.06 sec + 83/114 Test #118: Test_002.readTypes_interlaved_fail_2 ............ Passed 0.09 sec test 119 Start 119: Test_002.readTypes_interlaved_pass @@ -8948,7 +8978,7 @@ 119: Test timeout computed to be: 1500 119: running 002.readTypes_interlaved_pass 119: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BTB input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq 1>./actual/002.readTypes_interlaved_pass/load.stdout 2>./actual/002.readTypes_interlaved_pass/load.stderr - 84/114 Test #119: Test_002.readTypes_interlaved_pass .............. Passed 0.11 sec + 84/114 Test #119: Test_002.readTypes_interlaved_pass .............. Passed 0.27 sec test 120 Start 120: Test_003.files_not_exists @@ -8957,7 +8987,7 @@ 120: Test timeout computed to be: 1500 120: running 003.files_not_exists 120: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp dummy1.fq 1>./actual/003.files_not_exists/load.stdout 2>./actual/003.files_not_exists/load.stderr - 85/114 Test #120: Test_003.files_not_exists ....................... Passed 0.17 sec + 85/114 Test #120: Test_003.files_not_exists ....................... Passed 0.14 sec test 121 Start 121: Test_003.files_not_valid @@ -8966,7 +8996,7 @@ 121: Test timeout computed to be: 1500 121: running 003.files_not_valid 121: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/003.empty.fq 1>./actual/003.files_not_valid/load.stdout 2>./actual/003.files_not_valid/load.stderr - 86/114 Test #121: Test_003.files_not_valid ........................ Passed 0.18 sec + 86/114 Test #121: Test_003.files_not_valid ........................ Passed 0.23 sec test 122 Start 122: Test_003.files_readpairs @@ -8975,7 +9005,7 @@ 122: Test timeout computed to be: 1500 122: running 003.files_readpairs 122: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq,input/003.t3_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq 1>./actual/003.files_readpairs/load.stdout 2>./actual/003.files_readpairs/load.stderr - 87/114 Test #122: Test_003.files_readpairs ........................ Passed 0.23 sec + 87/114 Test #122: Test_003.files_readpairs ........................ Passed 0.40 sec test 123 Start 123: Test_003.files_mixed @@ -8984,7 +9014,7 @@ 123: Test timeout computed to be: 1500 123: running 003.files_mixed 123: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/005.offset0_1.fq input/001.R1.fastq 1>./actual/003.files_mixed/load.stdout 2>./actual/003.files_mixed/load.stderr - 88/114 Test #123: Test_003.files_mixed ............................ Passed 0.14 sec + 88/114 Test #123: Test_003.files_mixed ............................ Passed 0.15 sec test 124 Start 124: Test_003.files_mixed_cluster @@ -9002,7 +9032,7 @@ 125: Test timeout computed to be: 1500 125: running 003.files_10x_mixed 125: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/003.t_I1.fastq input/003.t_R1.fastq input/003.t_R2.fastq input/003._I1.fastq input/003.R1.fastq input/003.R2.fastq 1>./actual/003.files_10x_mixed/load.stdout 2>./actual/003.files_10x_mixed/load.stderr - 90/114 Test #125: Test_003.files_10x_mixed ........................ Passed 0.27 sec + 90/114 Test #125: Test_003.files_10x_mixed ........................ Passed 0.25 sec test 126 Start 126: Test_003.readTypes_10x @@ -9011,7 +9041,7 @@ 126: Test timeout computed to be: 1500 126: running 003.readTypes_10x 126: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/003.t_R1.fastq input/003.t_R1.fastq input/003.t_I1.fastq 1>./actual/003.readTypes_10x/load.stdout 2>./actual/003.readTypes_10x/load.stderr - 91/114 Test #126: Test_003.readTypes_10x .......................... Passed 0.20 sec + 91/114 Test #126: Test_003.readTypes_10x .......................... Passed 0.35 sec test 127 Start 127: Test_003.wrong_pairing @@ -9020,7 +9050,7 @@ 127: Test timeout computed to be: 1500 127: running 003.wrong_pairing 127: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq 1>./actual/003.wrong_pairing/load.stdout 2>./actual/003.wrong_pairing/load.stderr - 92/114 Test #127: Test_003.wrong_pairing .......................... Passed 0.11 sec + 92/114 Test #127: Test_003.wrong_pairing .......................... Passed 0.15 sec test 128 Start 128: Test_004.truncated.fail @@ -9029,7 +9059,7 @@ 128: Test timeout computed to be: 1500 128: running 004.truncated.fail 128: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/004.truncated_1.fq.gz input/004.truncated_2.fq.gz 1>./actual/004.truncated.fail/load.stdout 2>./actual/004.truncated.fail/load.stderr - 93/114 Test #128: Test_004.truncated.fail ......................... Passed 1.67 sec + 93/114 Test #128: Test_004.truncated.fail ......................... Passed 4.27 sec test 129 Start 129: Test_004.truncated.pass @@ -9038,7 +9068,7 @@ 129: Test timeout computed to be: 1500 129: running 004.truncated.pass 129: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --allowEarlyFileEnd input/004.truncated_1.fq.gz input/004.truncated_2.fq.gz 1>./actual/004.truncated.pass/load.stdout 2>./actual/004.truncated.pass/load.stderr - 94/114 Test #129: Test_004.truncated.pass ......................... Passed 2.14 sec + 94/114 Test #129: Test_004.truncated.pass ......................... Passed 5.64 sec test 130 Start 130: Test_005.offset0 @@ -9047,7 +9077,7 @@ 130: Test timeout computed to be: 1500 130: running 005.offset0 130: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/005.offset0_1.fq input/005.offset0_2.fq 1>./actual/005.offset0/load.stdout 2>./actual/005.offset0/load.stderr - 95/114 Test #130: Test_005.offset0 ................................ Passed 0.11 sec + 95/114 Test #130: Test_005.offset0 ................................ Passed 0.28 sec test 131 Start 131: Test_005.offset64 @@ -9056,7 +9086,7 @@ 131: Test timeout computed to be: 1500 131: running 005.offset64 131: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/005.offset64_1.fq input/005.offset64_2.fq 1>./actual/005.offset64/load.stdout 2>./actual/005.offset64/load.stderr - 96/114 Test #131: Test_005.offset64 ............................... Passed 0.11 sec + 96/114 Test #131: Test_005.offset64 ............................... Passed 0.22 sec test 132 Start 132: Test_006.duplicate @@ -9065,7 +9095,7 @@ 132: Test timeout computed to be: 1500 132: running 006.duplicate 132: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/006.duplicate.fq 1>./actual/006.duplicate/load.stdout 2>./actual/006.duplicate/load.stderr - 97/114 Test #132: Test_006.duplicate .............................. Passed 0.11 sec + 97/114 Test #132: Test_006.duplicate .............................. Passed 0.23 sec test 133 Start 133: Test_007.digest.udenfined @@ -9074,7 +9104,7 @@ 133: Test timeout computed to be: 1500 133: running 007.digest.udenfined 133: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --digest input/001.read.unsupported.fq 1>./actual/007.digest.udenfined/load.stdout 2>./actual/007.digest.udenfined/load.stderr - 98/114 Test #133: Test_007.digest.udenfined ....................... Passed 0.07 sec + 98/114 Test #133: Test_007.digest.udenfined ....................... Passed 0.19 sec test 134 Start 134: Test_007.digest.multiple @@ -9083,7 +9113,7 @@ 134: Test timeout computed to be: 1500 134: running 007.digest.multiple 134: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --digest input/003.t_R1.fastq input/003.t_R1.fastq input/003.t_I1.fastq 1>./actual/007.digest.multiple/load.stdout 2>./actual/007.digest.multiple/load.stderr - 99/114 Test #134: Test_007.digest.multiple ........................ Passed 0.09 sec + 99/114 Test #134: Test_007.digest.multiple ........................ Passed 0.28 sec test 135 Start 135: Test_007.digest.groups @@ -9092,7 +9122,7 @@ 135: Test timeout computed to be: 1500 135: running 007.digest.groups 135: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --digest input/003.t_R1.fastq.gz input/003.t2_R1.fastq input/003.t3_R1.fastq input/003.t_R2.fastq.gz input/003.t2_R2.fastq input/003.t3_R2.fastq input/003.t_I1.fastq.gz input/003.t2_I1.fastq input/003.t3_I1.fastq 1>./actual/007.digest.groups/load.stdout 2>./actual/007.digest.groups/load.stderr -100/114 Test #135: Test_007.digest.groups .......................... Passed 0.19 sec +100/114 Test #135: Test_007.digest.groups .......................... Passed 0.49 sec test 136 Start 136: Test_007.digest.error @@ -9101,7 +9131,7 @@ 136: Test timeout computed to be: 1500 136: running 007.digest.error 136: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --digest input/001.read.invalid_quality0.fq 1>./actual/007.digest.error/load.stdout 2>./actual/007.digest.error/load.stderr -101/114 Test #136: Test_007.digest.error ........................... Passed 0.10 sec +101/114 Test #136: Test_007.digest.error ........................... Passed 0.17 sec test 137 Start 137: Test_008.telemetry_pass @@ -9110,7 +9140,7 @@ 137: Test timeout computed to be: 1500 137: running 008.telemetry_pass 137: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq,input/003.t3_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq -t ./actual/008.telemetry_pass/telemetry 1>./actual/008.telemetry_pass/load.stdout 2>./actual/008.telemetry_pass/load.stderr -102/114 Test #137: Test_008.telemetry_pass ......................... Passed 0.25 sec +102/114 Test #137: Test_008.telemetry_pass ......................... Passed 0.36 sec test 138 Start 138: Test_009.more_than_4_per_spot @@ -9119,7 +9149,7 @@ 138: Test timeout computed to be: 1500 138: running 009.more_than_4_per_spot 138: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --debug input/009.test_I1_001.fastq input/009.test_R1_001.fastq input/009.test_R2_001.fastq input/009.test_R3_001.fastq 1>./actual/009.more_than_4_per_spot/load.stdout 2>./actual/009.more_than_4_per_spot/load.stderr -103/114 Test #138: Test_009.more_than_4_per_spot ................... Passed 0.35 sec +103/114 Test #138: Test_009.more_than_4_per_spot ................... Passed 0.28 sec test 139 Start 139: Test_010.errors.invalid_seq_pass1 @@ -9128,7 +9158,7 @@ 139: Test timeout computed to be: 1500 139: running 010.errors.invalid_seq_pass1 139: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/010.errors.invalid_seq.fq 1>./actual/010.errors.invalid_seq_pass1/load.stdout 2>./actual/010.errors.invalid_seq_pass1/load.stderr -104/114 Test #139: Test_010.errors.invalid_seq_pass1 ............... Passed 0.11 sec +104/114 Test #139: Test_010.errors.invalid_seq_pass1 ............... Passed 0.20 sec test 140 Start 140: Test_010.errors.invalid_seq_pass2 @@ -9137,7 +9167,7 @@ 140: Test timeout computed to be: 1500 140: running 010.errors.invalid_seq_pass2 140: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 5 input/010.errors.invalid_seq.fq 1>./actual/010.errors.invalid_seq_pass2/load.stdout 2>./actual/010.errors.invalid_seq_pass2/load.stderr -105/114 Test #140: Test_010.errors.invalid_seq_pass2 ............... Passed 0.13 sec +105/114 Test #140: Test_010.errors.invalid_seq_pass2 ............... Passed 0.23 sec test 141 Start 141: Test_010.errors.invalid_seq_fail @@ -9146,7 +9176,7 @@ 141: Test timeout computed to be: 1500 141: running 010.errors.invalid_seq_fail 141: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 3 input/010.errors.invalid_seq.fq 1>./actual/010.errors.invalid_seq_fail/load.stdout 2>./actual/010.errors.invalid_seq_fail/load.stderr -106/114 Test #141: Test_010.errors.invalid_seq_fail ................ Passed 0.11 sec +106/114 Test #141: Test_010.errors.invalid_seq_fail ................ Passed 0.17 sec test 142 Start 142: Test_011.nanopore.3 @@ -9155,7 +9185,7 @@ 142: Test timeout computed to be: 1500 142: running 011.nanopore.3 142: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/011.nanopore.3.fq 1>./actual/011.nanopore.3/load.stdout 2>./actual/011.nanopore.3/load.stderr -107/114 Test #142: Test_011.nanopore.3 ............................. Passed 0.16 sec +107/114 Test #142: Test_011.nanopore.3 ............................. Passed 0.24 sec test 143 Start 143: Test_012.qualities @@ -9164,7 +9194,7 @@ 143: Test timeout computed to be: 1500 143: running 012.qualities 143: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/012.test_I1_001.fastq input/012.test_R1_001.fastq input/012.test_R2_001.fastq input/012.test2_I1_001.fastq input/012.test2_R1_001.fastq input/012.test2_R2_001.fastq 1>./actual/012.qualities/load.stdout 2>./actual/012.qualities/load.stderr -108/114 Test #143: Test_012.qualities .............................. Passed 0.25 sec +108/114 Test #143: Test_012.qualities .............................. Passed 0.36 sec test 144 Start 144: Test_013.no-reads @@ -9173,7 +9203,7 @@ 144: Test timeout computed to be: 1500 144: running 013.no-reads 144: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/013.t_I1.fastq input/013.t_I2.fastq input/013.t_R1.fastq input/013.t_R2.fastq 1>./actual/013.no-reads/load.stdout 2>./actual/013.no-reads/load.stderr -109/114 Test #144: Test_013.no-reads ............................... Passed 16.50 sec +109/114 Test #144: Test_013.no-reads ............................... Passed 54.69 sec test 145 Start 145: Test_Align_samextract @@ -9184,7 +9214,7 @@ 145: Test_Qual_Decode (0 s) 145: Fast_Sequence (0 s) 145: Fast_u32toa (0 s) -145: Fast_i32toa (0 s) +145: Fast_i32toa (1 s) 145: Fast_strtoi64 (0 s) 145: Decode_Cigar (0 s) 145: Check_Cigar (0 s) @@ -9264,40 +9294,40 @@ 145: 145: Fuzz_Hangs (0 s) 145: -145: *** No errors detected (1 s total) -110/114 Test #145: Test_Align_samextract ........................... Passed 1.05 sec +145: *** No errors detected (2 s total) +110/114 Test #145: Test_Align_samextract ........................... Passed 2.64 sec test 147 Start 147: Test_Scripts_prepare-sra-names 147: Test command: /usr/bin/perl "test-prepare-sra-names.pl" 147: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/scripts 147: Test timeout computed to be: 1500 -111/114 Test #147: Test_Scripts_prepare-sra-names .................. Passed 1.35 sec +111/114 Test #147: Test_Scripts_prepare-sra-names .................. Passed 1.55 sec test 148 Start 148: Test_Scripts_fix-sra-names 148: Test command: /usr/bin/perl "test-fix-sra-names.pl" 148: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/scripts 148: Test timeout computed to be: 1500 -112/114 Test #148: Test_Scripts_fix-sra-names ...................... Passed 0.57 sec +112/114 Test #148: Test_Scripts_fix-sra-names ...................... Passed 0.72 sec test 149 Start 149: Test_Scripts_prepare-sra-names-py 149: Test command: /usr/bin/perl "test-prepare-sra-names-py.pl" 149: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/scripts 149: Test timeout computed to be: 1500 -113/114 Test #149: Test_Scripts_prepare-sra-names-py ............... Passed 2.16 sec +113/114 Test #149: Test_Scripts_prepare-sra-names-py ............... Passed 3.89 sec test 150 Start 150: Test_Scripts_fix-sra-names-py 150: Test command: /usr/bin/perl "test-fix-sra-names-py.pl" 150: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/scripts 150: Test timeout computed to be: 1500 -114/114 Test #150: Test_Scripts_fix-sra-names-py ................... Passed 1.31 sec +114/114 Test #150: Test_Scripts_fix-sra-names-py ................... Passed 2.24 sec 100% tests passed, 0 tests failed out of 114 -Total Test time (real) = 61.72 sec +Total Test time (real) = 138.70 sec make[1]: Leaving directory '/build/sra-sdk-3.0.3+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake @@ -9308,7 +9338,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/sra-sdk-3.0.3+dfsg' dh_auto_install - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/sra-sdk-3.0.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/sra-sdk-3.0.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/sra-sdk-3.0.3+dfsg -B/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -9819,229 +9849,229 @@ done ls -l debian/tmp/usr/bin total 81692 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 abi-dump -> abi-dump.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 abi-dump.3 -> abi-dump.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 267544 Aug 24 00:06 abi-dump.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 abi-load -> abi-load.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 abi-load.3 -> abi-load.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 635568 Aug 24 00:07 abi-load.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 align-cache -> align-cache.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 17 Aug 24 00:18 align-cache.3 -> align-cache.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 244864 Aug 24 00:07 align-cache.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 align-info -> align-info.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 align-info.3 -> align-info.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 95944 Aug 24 00:06 align-info.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 bam-load -> bam-load.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 bam-load.3 -> bam-load.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 12579712 Aug 24 00:12 bam-load.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 cache-mgr -> cache-mgr.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 cache-mgr.3 -> cache-mgr.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 124016 Aug 24 00:06 cache-mgr.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 ccextract -> ccextract.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 ccextract.3 -> ccextract.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 271856 Aug 24 00:07 ccextract.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 cg-load -> cg-load.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 cg-load.3 -> cg-load.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 654456 Aug 24 00:07 cg-load.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 check-corrupt -> check-corrupt.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 19 Aug 24 00:18 check-corrupt.3 -> check-corrupt.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 248880 Aug 24 00:06 check-corrupt.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 copycat -> copycat.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 copycat.3 -> copycat.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 462592 Aug 24 00:07 copycat.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 crc32sum -> crc32sum.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 crc32sum.3 -> crc32sum.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 79096 Aug 24 00:07 crc32sum.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 22 Aug 24 00:18 dump-blob-boundaries -> dump-blob-boundaries.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 26 Aug 24 00:18 dump-blob-boundaries.3 -> dump-blob-boundaries.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 31368 Aug 24 00:06 dump-blob-boundaries.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 fastconv -> fastconv.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 fastconv.3 -> fastconv.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 4919216 Aug 24 00:11 fastconv.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 fasterq-dump -> fasterq-dump.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 822992 Aug 24 00:06 fasterq-dump-orig.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 fasterq-dump.3 -> fasterq-dump.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 fasterq-dump.3.0.3 -> sratools.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 fastq-dump -> fastq-dump.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 347056 Aug 24 00:06 fastq-dump-orig.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 fastq-dump.3 -> fastq-dump.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 fastq-dump.3.0.3 -> sratools.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 fastq-load -> fastq-load.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 fastq-load.3 -> fastq-load.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 691240 Aug 24 00:07 fastq-load.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 general-loader -> general-loader.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 20 Aug 24 00:18 general-loader.3 -> general-loader.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 1419528 Aug 24 00:07 general-loader.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 helicos-load -> helicos-load.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 helicos-load.3 -> helicos-load.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 602456 Aug 24 00:07 helicos-load.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 illumina-dump -> illumina-dump.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 19 Aug 24 00:18 illumina-dump.3 -> illumina-dump.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 250040 Aug 24 00:06 illumina-dump.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 illumina-load -> illumina-load.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 19 Aug 24 00:18 illumina-load.3 -> illumina-load.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 647480 Aug 24 00:07 illumina-load.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 5 Aug 24 00:18 kar -> kar.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 6 Aug 24 00:18 kar+ -> kar+.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 kar+.3 -> kar+.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 236680 Aug 24 00:06 kar+.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 kar+meta -> kar+meta.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 kar+meta.3 -> kar+meta.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 158024 Aug 24 00:06 kar+meta.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 kar.3 -> kar.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 190512 Aug 24 00:06 kar.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 kdb-index -> kdb-index.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 kdb-index.3 -> kdb-index.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 78168 Aug 24 00:07 kdb-index.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 kdbmeta -> kdbmeta.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 kdbmeta.3 -> kdbmeta.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 123960 Aug 24 00:06 kdbmeta.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 latf-load -> latf-load.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 latf-load.3 -> latf-load.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 504056 Aug 24 00:08 latf-load.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 make-read-filter -> make-read-filter.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 22 Aug 24 00:18 make-read-filter.3 -> make-read-filter.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 153808 Aug 24 00:07 make-read-filter.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 7 Aug 24 00:18 md5cp -> md5cp.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 md5cp.3 -> md5cp.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 89576 Aug 24 00:07 md5cp.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 meta-cmp -> meta-cmp.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 meta-cmp.3 -> meta-cmp.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 81736 Aug 24 00:07 meta-cmp.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 meta-copy -> meta-copy.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 meta-copy.3 -> meta-copy.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 81696 Aug 24 00:07 meta-copy.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 ngs-pileup -> ngs-pileup.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 ngs-pileup.3 -> ngs-pileup.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 2582160 Aug 24 00:08 ngs-pileup.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 pacbio-correct -> pacbio-correct.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 20 Aug 24 00:18 pacbio-correct.3 -> pacbio-correct.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 75952 Aug 24 00:07 pacbio-correct.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 pacbio-load -> pacbio-load.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 17 Aug 24 00:18 pacbio-load.3 -> pacbio-load.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 474872 Aug 24 00:07 pacbio-load.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 pacbio-loadxml -> pacbio-loadxml.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 20 Aug 24 00:18 pacbio-loadxml.3 -> pacbio-loadxml.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 581984 Aug 24 00:07 pacbio-loadxml.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 pileup-stats -> pileup-stats.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 pileup-stats.3 -> pileup-stats.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 2788008 Aug 24 00:09 pileup-stats.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 prefetch -> prefetch.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 460656 Aug 24 00:08 prefetch-orig.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 prefetch.3 -> prefetch.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 prefetch.3.0.3 -> sratools.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 rcexplain -> rcexplain.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 rcexplain.3 -> rcexplain.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 63288 Aug 24 00:06 rcexplain.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 20 Aug 24 00:18 read-filter-redact -> read-filter-redact.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 24 Aug 24 00:18 read-filter-redact.3 -> read-filter-redact.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 110800 Aug 24 00:07 read-filter-redact.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 ref-variation -> ref-variation.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 19 Aug 24 00:18 ref-variation.3 -> ref-variation.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 2937528 Aug 24 00:09 ref-variation.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 rowwritetest -> rowwritetest.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 rowwritetest.3 -> rowwritetest.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 88120 Aug 24 00:07 rowwritetest.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sam-dump -> sam-dump.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 820032 Aug 24 00:06 sam-dump-orig.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sam-dump.3 -> sam-dump.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sam-dump.3.0.3 -> sratools.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 samview -> samview.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 samview-util -> samview-util.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 samview-util.3 -> samview-util.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 64064 Aug 24 00:07 samview-util.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 samview.3 -> samview.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 301904 Aug 24 00:07 samview.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 schema-replace -> schema-replace.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 20 Aug 24 00:18 schema-replace.3 -> schema-replace.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 82840 Aug 24 00:07 schema-replace.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sff-dump -> sff-dump.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sff-dump.3 -> sff-dump.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 229576 Aug 24 00:06 sff-dump.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sff-load -> sff-load.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sff-load.3 -> sff-load.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 645864 Aug 24 00:07 sff-load.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 7 Aug 24 00:18 sharq -> sharq.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 sharq.3 -> sharq.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 18347328 Aug 24 00:14 sharq.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sortreadtest -> sortreadtest.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 sortreadtest.3 -> sortreadtest.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 79584 Aug 24 00:07 sortreadtest.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 sra-pileup -> sra-pileup.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 439704 Aug 24 00:06 sra-pileup-orig.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 sra-pileup.3 -> sra-pileup.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sra-pileup.3.0.3 -> sratools.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 sra-search -> sra-search.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 sra-search.3 -> sra-search.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 4015448 Aug 24 00:09 sra-search.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sra-sort -> sra-sort.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 sra-sort-cg -> sra-sort-cg.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 17 Aug 24 00:18 sra-sort-cg.3 -> sra-sort-cg.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 804496 Aug 24 00:07 sra-sort-cg.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sra-sort.3 -> sra-sort.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 804568 Aug 24 00:07 sra-sort.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sra-stat -> sra-stat.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sra-stat.3 -> sra-stat.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 317000 Aug 24 00:07 sra-stat.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 srapath -> srapath.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 252568 Aug 24 00:06 srapath-orig.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 srapath.3 -> srapath.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 srapath.3.0.3 -> sratools.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sratools -> sratools.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sratools.3 -> sratools.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 5112800 Aug 24 00:09 sratools.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 srf-load -> srf-load.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 srf-load.3 -> srf-load.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 824440 Aug 24 00:07 srf-load.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 test-download -> test-download.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 19 Aug 24 00:18 test-download.3 -> test-download.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 88664 Aug 24 00:07 test-download.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 24 Aug 24 00:18 test-read-write-cursor -> test-read-write-cursor.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 28 Aug 24 00:18 test-read-write-cursor.3 -> test-read-write-cursor.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 75216 Aug 24 00:07 test-read-write-cursor.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 test-sra -> test-sra.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 test-sra.3 -> test-sra.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 329568 Aug 24 00:06 test-sra.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 8 Aug 24 00:18 testld -> testld.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 testld.3 -> testld.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 76408 Aug 24 00:07 testld.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 txt2kdb -> txt2kdb.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 txt2kdb.3 -> txt2kdb.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 82720 Aug 24 00:07 txt2kdb.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 var-expand -> var-expand.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 var-expand.3 -> var-expand.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 1988808 Aug 24 00:08 var-expand.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 vdb-config -> vdb-config.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 vdb-config.3 -> vdb-config.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 3392176 Aug 24 00:10 vdb-config.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 vdb-copy -> vdb-copy.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-copy.3 -> vdb-copy.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 326936 Aug 24 00:07 vdb-copy.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 vdb-decrypt -> vdb-decrypt.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 17 Aug 24 00:18 vdb-decrypt.3 -> vdb-decrypt.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 121384 Aug 24 00:06 vdb-decrypt.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 vdb-diff -> vdb-diff.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-diff.3 -> vdb-diff.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 150176 Aug 24 00:07 vdb-diff.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 vdb-dump -> vdb-dump.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 818504 Aug 24 00:07 vdb-dump-orig.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-dump.3 -> vdb-dump.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-dump.3.0.3 -> sratools.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 vdb-encrypt -> vdb-encrypt.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 17 Aug 24 00:18 vdb-encrypt.3 -> vdb-encrypt.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 119752 Aug 24 00:06 vdb-encrypt.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 vdb-lock -> vdb-lock.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-lock.3 -> vdb-lock.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 68256 Aug 24 00:07 vdb-lock.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 vdb-sql -> vdb-sql.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 vdb-sql.3 -> vdb-sql.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 5170312 Aug 24 00:11 vdb-sql.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 vdb-unlock -> vdb-unlock.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 vdb-unlock.3 -> vdb-unlock.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 68272 Aug 24 00:07 vdb-unlock.3.0.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-validate -> vdb-validate.3 -lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 vdb-validate.3 -> vdb-validate.3.0.3 --rwxr-xr-x 1 pbuilder1 pbuilder1 224008 Aug 24 00:06 vdb-validate.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 abi-dump -> abi-dump.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 abi-dump.3 -> abi-dump.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 267544 Jul 23 20:07 abi-dump.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 abi-load -> abi-load.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 abi-load.3 -> abi-load.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 635568 Jul 23 20:08 abi-load.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 align-cache -> align-cache.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 17 Jul 23 20:34 align-cache.3 -> align-cache.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 244864 Jul 23 20:09 align-cache.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 12 Jul 23 20:34 align-info -> align-info.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 align-info.3 -> align-info.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 95944 Jul 23 20:07 align-info.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 bam-load -> bam-load.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 bam-load.3 -> bam-load.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 12579712 Jul 23 20:17 bam-load.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 11 Jul 23 20:34 cache-mgr -> cache-mgr.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 15 Jul 23 20:34 cache-mgr.3 -> cache-mgr.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 124016 Jul 23 20:07 cache-mgr.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 11 Jul 23 20:34 ccextract -> ccextract.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 15 Jul 23 20:34 ccextract.3 -> ccextract.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 271856 Jul 23 20:09 ccextract.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 9 Jul 23 20:34 cg-load -> cg-load.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 cg-load.3 -> cg-load.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 654456 Jul 23 20:09 cg-load.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 15 Jul 23 20:34 check-corrupt -> check-corrupt.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 19 Jul 23 20:34 check-corrupt.3 -> check-corrupt.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 248880 Jul 23 20:07 check-corrupt.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 9 Jul 23 20:34 copycat -> copycat.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 copycat.3 -> copycat.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 462592 Jul 23 20:09 copycat.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 crc32sum -> crc32sum.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 crc32sum.3 -> crc32sum.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 79096 Jul 23 20:09 crc32sum.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 22 Jul 23 20:34 dump-blob-boundaries -> dump-blob-boundaries.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 26 Jul 23 20:34 dump-blob-boundaries.3 -> dump-blob-boundaries.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 31368 Jul 23 20:07 dump-blob-boundaries.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 fastconv -> fastconv.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 fastconv.3 -> fastconv.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 4919216 Jul 23 20:15 fastconv.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 fasterq-dump -> fasterq-dump.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 822992 Jul 23 20:08 fasterq-dump-orig.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 18 Jul 23 20:34 fasterq-dump.3 -> fasterq-dump.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 fasterq-dump.3.0.3 -> sratools.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 12 Jul 23 20:34 fastq-dump -> fastq-dump.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 347056 Jul 23 20:07 fastq-dump-orig.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 fastq-dump.3 -> fastq-dump.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 fastq-dump.3.0.3 -> sratools.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 12 Jul 23 20:34 fastq-load -> fastq-load.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 fastq-load.3 -> fastq-load.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 691240 Jul 23 20:08 fastq-load.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 general-loader -> general-loader.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 20 Jul 23 20:34 general-loader.3 -> general-loader.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 1419528 Jul 23 20:10 general-loader.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 helicos-load -> helicos-load.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 18 Jul 23 20:34 helicos-load.3 -> helicos-load.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 602456 Jul 23 20:08 helicos-load.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 15 Jul 23 20:34 illumina-dump -> illumina-dump.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 19 Jul 23 20:34 illumina-dump.3 -> illumina-dump.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 250040 Jul 23 20:07 illumina-dump.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 15 Jul 23 20:34 illumina-load -> illumina-load.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 19 Jul 23 20:34 illumina-load.3 -> illumina-load.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 647480 Jul 23 20:08 illumina-load.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 5 Jul 23 20:34 kar -> kar.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 6 Jul 23 20:34 kar+ -> kar+.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 kar+.3 -> kar+.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 236680 Jul 23 20:08 kar+.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 kar+meta -> kar+meta.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 kar+meta.3 -> kar+meta.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 158024 Jul 23 20:08 kar+meta.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 9 Jul 23 20:34 kar.3 -> kar.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 190512 Jul 23 20:07 kar.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 11 Jul 23 20:34 kdb-index -> kdb-index.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 15 Jul 23 20:34 kdb-index.3 -> kdb-index.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 78168 Jul 23 20:09 kdb-index.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 9 Jul 23 20:34 kdbmeta -> kdbmeta.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 kdbmeta.3 -> kdbmeta.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 123960 Jul 23 20:07 kdbmeta.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 11 Jul 23 20:34 latf-load -> latf-load.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 15 Jul 23 20:34 latf-load.3 -> latf-load.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 504056 Jul 23 20:11 latf-load.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 18 Jul 23 20:34 make-read-filter -> make-read-filter.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 22 Jul 23 20:34 make-read-filter.3 -> make-read-filter.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 153808 Jul 23 20:09 make-read-filter.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 7 Jul 23 20:34 md5cp -> md5cp.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 11 Jul 23 20:34 md5cp.3 -> md5cp.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 89576 Jul 23 20:09 md5cp.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 meta-cmp -> meta-cmp.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 meta-cmp.3 -> meta-cmp.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 81736 Jul 23 20:09 meta-cmp.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 11 Jul 23 20:34 meta-copy -> meta-copy.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 15 Jul 23 20:34 meta-copy.3 -> meta-copy.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 81696 Jul 23 20:09 meta-copy.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 12 Jul 23 20:34 ngs-pileup -> ngs-pileup.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 ngs-pileup.3 -> ngs-pileup.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 2582160 Jul 23 20:11 ngs-pileup.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 pacbio-correct -> pacbio-correct.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 20 Jul 23 20:34 pacbio-correct.3 -> pacbio-correct.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 75952 Jul 23 20:09 pacbio-correct.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 pacbio-load -> pacbio-load.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 17 Jul 23 20:34 pacbio-load.3 -> pacbio-load.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 474872 Jul 23 20:09 pacbio-load.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 pacbio-loadxml -> pacbio-loadxml.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 20 Jul 23 20:34 pacbio-loadxml.3 -> pacbio-loadxml.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 581984 Jul 23 20:09 pacbio-loadxml.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 pileup-stats -> pileup-stats.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 18 Jul 23 20:34 pileup-stats.3 -> pileup-stats.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 2788008 Jul 23 20:12 pileup-stats.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 prefetch -> prefetch.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 460656 Jul 23 20:11 prefetch-orig.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 prefetch.3 -> prefetch.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 prefetch.3.0.3 -> sratools.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 11 Jul 23 20:34 rcexplain -> rcexplain.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 15 Jul 23 20:34 rcexplain.3 -> rcexplain.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 63288 Jul 23 20:07 rcexplain.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 20 Jul 23 20:34 read-filter-redact -> read-filter-redact.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 24 Jul 23 20:34 read-filter-redact.3 -> read-filter-redact.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 110800 Jul 23 20:09 read-filter-redact.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 15 Jul 23 20:34 ref-variation -> ref-variation.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 19 Jul 23 20:34 ref-variation.3 -> ref-variation.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 2937528 Jul 23 20:12 ref-variation.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 rowwritetest -> rowwritetest.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 18 Jul 23 20:34 rowwritetest.3 -> rowwritetest.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 88120 Jul 23 20:09 rowwritetest.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 sam-dump -> sam-dump.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 820032 Jul 23 20:08 sam-dump-orig.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 sam-dump.3 -> sam-dump.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 sam-dump.3.0.3 -> sratools.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 9 Jul 23 20:34 samview -> samview.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 samview-util -> samview-util.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 18 Jul 23 20:34 samview-util.3 -> samview-util.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 64064 Jul 23 20:09 samview-util.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 samview.3 -> samview.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 301904 Jul 23 20:08 samview.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 schema-replace -> schema-replace.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 20 Jul 23 20:34 schema-replace.3 -> schema-replace.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 82840 Jul 23 20:09 schema-replace.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 sff-dump -> sff-dump.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 sff-dump.3 -> sff-dump.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 229576 Jul 23 20:07 sff-dump.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 sff-load -> sff-load.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 sff-load.3 -> sff-load.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 645864 Jul 23 20:08 sff-load.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 7 Jul 23 20:34 sharq -> sharq.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 11 Jul 23 20:34 sharq.3 -> sharq.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 18347328 Jul 23 20:23 sharq.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 sortreadtest -> sortreadtest.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 18 Jul 23 20:34 sortreadtest.3 -> sortreadtest.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 79584 Jul 23 20:09 sortreadtest.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 12 Jul 23 20:34 sra-pileup -> sra-pileup.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 439704 Jul 23 20:07 sra-pileup-orig.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 sra-pileup.3 -> sra-pileup.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 sra-pileup.3.0.3 -> sratools.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 12 Jul 23 20:34 sra-search -> sra-search.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 sra-search.3 -> sra-search.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 4015448 Jul 23 20:12 sra-search.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 sra-sort -> sra-sort.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 sra-sort-cg -> sra-sort-cg.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 17 Jul 23 20:34 sra-sort-cg.3 -> sra-sort-cg.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 804496 Jul 23 20:09 sra-sort-cg.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 sra-sort.3 -> sra-sort.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 804568 Jul 23 20:09 sra-sort.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 sra-stat -> sra-stat.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 sra-stat.3 -> sra-stat.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 317000 Jul 23 20:08 sra-stat.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 9 Jul 23 20:34 srapath -> srapath.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 252568 Jul 23 20:07 srapath-orig.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 srapath.3 -> srapath.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 srapath.3.0.3 -> sratools.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 sratools -> sratools.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 sratools.3 -> sratools.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 5112800 Jul 23 20:11 sratools.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 srf-load -> srf-load.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 srf-load.3 -> srf-load.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 824440 Jul 23 20:09 srf-load.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 15 Jul 23 20:34 test-download -> test-download.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 19 Jul 23 20:34 test-download.3 -> test-download.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 88664 Jul 23 20:09 test-download.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 24 Jul 23 20:34 test-read-write-cursor -> test-read-write-cursor.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 28 Jul 23 20:34 test-read-write-cursor.3 -> test-read-write-cursor.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 75216 Jul 23 20:09 test-read-write-cursor.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 test-sra -> test-sra.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 test-sra.3 -> test-sra.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 329568 Jul 23 20:08 test-sra.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 8 Jul 23 20:34 testld -> testld.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 12 Jul 23 20:34 testld.3 -> testld.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 76408 Jul 23 20:09 testld.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 9 Jul 23 20:34 txt2kdb -> txt2kdb.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 txt2kdb.3 -> txt2kdb.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 82720 Jul 23 20:09 txt2kdb.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 12 Jul 23 20:34 var-expand -> var-expand.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 var-expand.3 -> var-expand.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 1988808 Jul 23 20:11 var-expand.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 12 Jul 23 20:34 vdb-config -> vdb-config.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 vdb-config.3 -> vdb-config.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 3392176 Jul 23 20:12 vdb-config.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 vdb-copy -> vdb-copy.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 vdb-copy.3 -> vdb-copy.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 326936 Jul 23 20:09 vdb-copy.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 vdb-decrypt -> vdb-decrypt.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 17 Jul 23 20:34 vdb-decrypt.3 -> vdb-decrypt.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 121384 Jul 23 20:07 vdb-decrypt.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 vdb-diff -> vdb-diff.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 vdb-diff.3 -> vdb-diff.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 150176 Jul 23 20:09 vdb-diff.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 vdb-dump -> vdb-dump.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 818504 Jul 23 20:08 vdb-dump-orig.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 vdb-dump.3 -> vdb-dump.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 vdb-dump.3.0.3 -> sratools.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 vdb-encrypt -> vdb-encrypt.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 17 Jul 23 20:34 vdb-encrypt.3 -> vdb-encrypt.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 119752 Jul 23 20:07 vdb-encrypt.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 10 Jul 23 20:34 vdb-lock -> vdb-lock.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 vdb-lock.3 -> vdb-lock.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 68256 Jul 23 20:09 vdb-lock.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 9 Jul 23 20:34 vdb-sql -> vdb-sql.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 13 Jul 23 20:34 vdb-sql.3 -> vdb-sql.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 5170312 Jul 23 20:15 vdb-sql.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 12 Jul 23 20:34 vdb-unlock -> vdb-unlock.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 16 Jul 23 20:34 vdb-unlock.3 -> vdb-unlock.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 68272 Jul 23 20:09 vdb-unlock.3.0.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 14 Jul 23 20:34 vdb-validate -> vdb-validate.3 +lrwxrwxrwx 1 pbuilder2 pbuilder2 18 Jul 23 20:34 vdb-validate.3 -> vdb-validate.3.0.3 +-rwxr-xr-x 1 pbuilder2 pbuilder2 224008 Jul 23 20:07 vdb-validate.3.0.3 cd debian/tmp/usr/bin && \ for bin in *-orig.* ; do \ base=${bin%-orig.*} && \ @@ -10348,35 +10378,35 @@ dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake -dpkg-shlibdeps: warning: symbol KVectorRelease used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol VBlobSize used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol KVectorGetFirstBool used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol DLListPopHead used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol xcCursorExhausted used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol VCursorCloseRow used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol PageMapIteratorDataOffset_Ext used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol xcIntegerOutOfBounds used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol xcParamNull used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol KNSManagerMake used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol xcParamUnexpected used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol xcCursorCreateFailed used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol VCursorOpenRow used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol xcWrongReadGroup used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol VPathRelease used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol VDBManagerOpenDBRead used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol ctx_what used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol BSTreeFirst used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol VCursorAddColumn used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol KDBManagerMakeRead used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: 133 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake -dpkg-gencontrol: warning: package libncbi-ngs-dev: substitution variable ${devlibs:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package libngs-jni: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: package libncbi-ngs-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'libngs-c++3' in '../libngs-c++3_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'libngs-c++3-dbgsym' in '../libngs-c++3-dbgsym_3.0.3+dfsg-6~deb12u1_amd64.deb'. -dpkg-deb: building package 'python3-ngs' in '../python3-ngs_3.0.3+dfsg-6~deb12u1_all.deb'. -dpkg-deb: building package 'libncbi-ngs-dev' in '../libncbi-ngs-dev_3.0.3+dfsg-6~deb12u1_amd64.deb'. -dpkg-deb: building package 'libngs-java-doc' in '../libngs-java-doc_3.0.3+dfsg-6~deb12u1_all.deb'. -dpkg-deb: building package 'sra-toolkit' in '../sra-toolkit_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'sra-toolkit-dbgsym' in '../sra-toolkit-dbgsym_3.0.3+dfsg-6~deb12u1_amd64.deb'. -dpkg-deb: building package 'libngs-java' in '../libngs-java_3.0.3+dfsg-6~deb12u1_amd64.deb'. -dpkg-deb: building package 'libncbi-ngs3-dbgsym' in '../libncbi-ngs3-dbgsym_3.0.3+dfsg-6~deb12u1_amd64.deb'. -dpkg-deb: building package 'libngs-jni' in '../libngs-jni_3.0.3+dfsg-6~deb12u1_amd64.deb'. -dpkg-deb: building package 'libncbi-ngs3' in '../libncbi-ngs3_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'libngs-c++-dev' in '../libngs-c++-dev_3.0.3+dfsg-6~deb12u1_amd64.deb'. +dpkg-deb: building package 'libncbi-ngs3' in '../libncbi-ngs3_3.0.3+dfsg-6~deb12u1_amd64.deb'. +dpkg-deb: building package 'sra-toolkit' in '../sra-toolkit_3.0.3+dfsg-6~deb12u1_amd64.deb'. +dpkg-deb: building package 'libngs-c++3' in '../libngs-c++3_3.0.3+dfsg-6~deb12u1_amd64.deb'. +dpkg-deb: building package 'libngs-jni' in '../libngs-jni_3.0.3+dfsg-6~deb12u1_amd64.deb'. +dpkg-deb: building package 'libngs-java-doc' in '../libngs-java-doc_3.0.3+dfsg-6~deb12u1_all.deb'. +dpkg-deb: building package 'libncbi-ngs-dev' in '../libncbi-ngs-dev_3.0.3+dfsg-6~deb12u1_amd64.deb'. +dpkg-deb: building package 'libncbi-ngs3-dbgsym' in '../libncbi-ngs3-dbgsym_3.0.3+dfsg-6~deb12u1_amd64.deb'. +dpkg-deb: building package 'python3-ngs' in '../python3-ngs_3.0.3+dfsg-6~deb12u1_all.deb'. +dpkg-deb: building package 'libngs-java' in '../libngs-java_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../sra-sdk_3.0.3+dfsg-6~deb12u1_amd64.buildinfo dpkg-genchanges --build=binary -O../sra-sdk_3.0.3+dfsg-6~deb12u1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -10384,12 +10414,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/556284/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/556284/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/428083 and its subdirectories -I: Current time: Sat Aug 24 00:20:55 -12 2024 -I: pbuilder-time-stamp: 1724502055 +I: removing directory /srv/workspace/pbuilder/556284 and its subdirectories +I: Current time: Sun Jul 23 20:40:06 +14 2023 +I: pbuilder-time-stamp: 1690094406