Diff of the two buildlogs: -- --- b1/build.log 2023-05-07 16:45:27.076900673 +0000 +++ b2/build.log 2023-05-07 17:13:31.539057116 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 8 10:54:17 -12 2024 -I: pbuilder-time-stamp: 1717887257 +I: Current time: Mon May 8 06:45:30 +14 2023 +I: pbuilder-time-stamp: 1683477930 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: copying [./genomicsdb_1.4.4.orig.tar.gz] I: copying [./genomicsdb_1.4.4-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Mar 26 01:44:40 2023 -12 +gpgv: Signature made Mon Mar 27 03:44:40 2023 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./genomicsdb_1.4.4-3.dsc: no acceptable signature found @@ -53,135 +53,167 @@ dpkg-source: info: applying using_debian_packaged_catch2.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2916162/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2304883/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 May 8 06:45 /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/2304883/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2304883/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='9454bbcc54ae47a8813d93b6af1a2859' - 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='2916162' - PS1='# ' - PS2='> ' + INVOCATION_ID=6b696d014cbc4f7f806d6b9e58f65110 + 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=2304883 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.wZIDzfgx/pbuilderrc_juGl --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.wZIDzfgx/b1 --logfile b1/build.log genomicsdb_1.4.4-3.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.wZIDzfgx/pbuilderrc_NfC4 --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.wZIDzfgx/b2 --logfile b2/build.log --extrapackages usrmerge genomicsdb_1.4.4-3.dsc' + SUDO_GID=111 + SUDO_UID=106 + 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 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) 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/2916162/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 03:20 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 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 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 03:33 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 03:33 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 09:55 sed + lrwxrwxrwx 1 root root 9 May 8 06:45 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 03:33 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/2304883/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -710,7 +742,7 @@ Get: 429 http://deb.debian.org/debian bookworm/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.1 [97.7 kB] Get: 430 http://deb.debian.org/debian bookworm/main amd64 testng all 6.9.12-4 [795 kB] Get: 431 http://deb.debian.org/debian bookworm/main amd64 uuid-dev amd64 2.38.1-5+b1 [39.9 kB] -Fetched 493 MB in 7s (69.0 MB/s) +Fetched 493 MB in 13s (39.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19596 files and directories currently installed.) @@ -2640,8 +2672,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/genomicsdb-1.4.4/ && 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 > ../genomicsdb_1.4.4-3_source.changes +I: user script /srv/workspace/pbuilder/2304883/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/2304883/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/genomicsdb-1.4.4/ && 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 > ../genomicsdb_1.4.4-3_source.changes dpkg-buildpackage: info: source package genomicsdb dpkg-buildpackage: info: source version 1.4.4-3 dpkg-buildpackage: info: source distribution unstable @@ -2797,7 +2840,7 @@ debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/genomicsdb-1.4.4' dh_auto_build - 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[2]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/genomicsdb-1.4.4 -B/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/CMakeFiles /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -2807,71 +2850,85 @@ make -f genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build.make genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-htslib /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/DependInfo.cmake --color= +make -f CMakeFiles/protobuf_ep.dir/build.make CMakeFiles/protobuf_ep.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/DependInfo.cmake --color= -make -f CMakeFiles/protobuf_ep.dir/build.make CMakeFiles/protobuf_ep.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/CMakeFiles/protobuf_ep.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build.make genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 0%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kfunc.c.o make -f genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build.make genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kfunc.c.o -MF CMakeFiles/genomicsdb-hts.dir/kfunc.c.o.d -o CMakeFiles/genomicsdb-hts.dir/kfunc.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/kfunc.c -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f 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-I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array.cc +[ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o [ 1%] Built target protobuf_ep -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kstring.c.o -MF CMakeFiles/genomicsdb-hts.dir/kstring.c.o.d -o CMakeFiles/genomicsdb-hts.dir/kstring.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/kstring.c -[ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/depend -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array.cc -[ 2%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o -[ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o +[ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array_iterator.cc make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/resources /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/DependInfo.cmake --color= -[ 2%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o -MF 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-DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp 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-I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array_schema.cc +[ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/knetfile.c.o +[ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kfunc.c.o -MF CMakeFiles/genomicsdb-hts.dir/kfunc.c.o.d -o CMakeFiles/genomicsdb-hts.dir/kfunc.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/kfunc.c make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 3%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/errmod.c.o +[ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bgzf.c.o make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP 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-I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/knetfile.c.o -MF CMakeFiles/genomicsdb-hts.dir/knetfile.c.o.d -o CMakeFiles/genomicsdb-hts.dir/knetfile.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/knetfile.c make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 4%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o -[ 4%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/faidx.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat 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-I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array_sorted_read_state.cc -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/faidx.c.o -MF CMakeFiles/genomicsdb-hts.dir/faidx.c.o.d -o CMakeFiles/genomicsdb-hts.dir/faidx.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/faidx.c -[ 4%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/header.c.o +[ 4%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/errmod.c.o [ 4%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 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/build/genomicsdb-1.4.4/genomicsdb-htslib/bcf_sr_sort.c cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array_sorted_write_state.cc -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile.c.o -MF CMakeFiles/genomicsdb-hts.dir/hfile.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hfile.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile.c +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bgzf.c.o -MF CMakeFiles/genomicsdb-hts.dir/bgzf.c.o.d -o CMakeFiles/genomicsdb-hts.dir/bgzf.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/bgzf.c +[ 4%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc +[ 5%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/errmod.c.o -MF CMakeFiles/genomicsdb-hts.dir/errmod.c.o.d -o CMakeFiles/genomicsdb-hts.dir/errmod.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/errmod.c [ 5%] Generating source/header files from .proto files cd /build/genomicsdb-1.4.4/src/resources && /usr/bin/protoc --cpp_out=/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources genomicsdb_coordinates.proto genomicsdb_callsets_mapping.proto genomicsdb_export_config.proto genomicsdb_import_config.proto genomicsdb_vid_mapping.proto -[ 5%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o -MF CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile_libcurl.c +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 5%] Built target PROTOBUF_GENERATED_CXX_TARGET make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/DependInfo.cmake --color= +[ 5%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/faidx.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/faidx.c.o -MF CMakeFiles/genomicsdb-hts.dir/faidx.c.o.d -o CMakeFiles/genomicsdb-hts.dir/faidx.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/faidx.c make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 5%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/variant_operations.cc +[ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile.c.o +[ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/header.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile.c.o -MF CMakeFiles/genomicsdb-hts.dir/hfile.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hfile.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile.c +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/header.c.o -MF CMakeFiles/genomicsdb-hts.dir/header.c.o.d -o CMakeFiles/genomicsdb-hts.dir/header.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/header.c +[ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o -MF CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile_libcurl.c +/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc: In function 'void TileDBUtils::print_md5_hash(unsigned char*, size_t)': +/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc:330:6: warning: 'unsigned char* TileDBUtils::MD5(const unsigned char*, size_t, unsigned char*)' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] + 330 | MD5(buffer, length, md); + | ~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc:327: +/usr/include/openssl/md5.h:52:38: note: declared here + 52 | OSSL_DEPRECATEDIN_3_0 unsigned char *MD5(const unsigned char *d, size_t n, + | ^~~ /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile_libcurl.c: In function 'libcurl_open': /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile_libcurl.c:1335:9: warning: 'CURLINFO_CONTENT_LENGTH_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, @@ -2880,52 +2937,30 @@ /usr/include/x86_64-linux-gnu/curl/curl.h:2858:3: note: declared here 2858 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 5%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/variant_operations.cc -[ 5%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o +[ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o -MF CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile_net.c -[ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts.c.o +[ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts.c.o -MF CMakeFiles/genomicsdb-hts.dir/hts.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hts.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hts.c -[ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts_os.c.o +[ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts_os.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts_os.c.o -MF CMakeFiles/genomicsdb-hts.dir/hts_os.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hts_os.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hts_os.c -[ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/md5.c.o -[ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/multipart.c.o +[ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/md5.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/md5.c.o -MF CMakeFiles/genomicsdb-hts.dir/md5.c.o.d -o CMakeFiles/genomicsdb-hts.dir/md5.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/md5.c +[ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/multipart.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/multipart.c.o -MF CMakeFiles/genomicsdb-hts.dir/multipart.c.o.d -o CMakeFiles/genomicsdb-hts.dir/multipart.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/multipart.c -[ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/realn.c.o -[ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/probaln.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/realn.c.o -MF CMakeFiles/genomicsdb-hts.dir/realn.c.o.d -o CMakeFiles/genomicsdb-hts.dir/realn.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/realn.c +[ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/probaln.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/probaln.c.o -MF CMakeFiles/genomicsdb-hts.dir/probaln.c.o.d -o CMakeFiles/genomicsdb-hts.dir/probaln.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/probaln.c -[ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/regidx.c.o +[ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/realn.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/realn.c.o -MF CMakeFiles/genomicsdb-hts.dir/realn.c.o.d -o CMakeFiles/genomicsdb-hts.dir/realn.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/realn.c +[ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/regidx.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/regidx.c.o -MF CMakeFiles/genomicsdb-hts.dir/regidx.c.o.d -o CMakeFiles/genomicsdb-hts.dir/regidx.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/regidx.c -[ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/region.c.o +[ 8%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec.cc +[ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/region.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/region.c.o -MF CMakeFiles/genomicsdb-hts.dir/region.c.o.d -o CMakeFiles/genomicsdb-hts.dir/region.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/region.c -[ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/sam.c.o +[ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/sam.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/sam.c.o -MF CMakeFiles/genomicsdb-hts.dir/sam.c.o.d -o CMakeFiles/genomicsdb-hts.dir/sam.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/sam.c -[ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o +[ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o -MF CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o.d -o CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/synced_bcf_reader.c -[ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o -[ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/tbx.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o -MF CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o.d -o CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/vcf_sweep.c -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/tbx.c.o -MF CMakeFiles/genomicsdb-hts.dir/tbx.c.o.d -o CMakeFiles/genomicsdb-hts.dir/tbx.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/tbx.c -[ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/textutils.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/textutils.c.o -MF CMakeFiles/genomicsdb-hts.dir/textutils.c.o.d -o CMakeFiles/genomicsdb-hts.dir/textutils.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/textutils.c -[ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o -[ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o -MF CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o.d -o CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/thread_pool.c -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf.c.o -MF CMakeFiles/genomicsdb-hts.dir/vcf.c.o.d -o CMakeFiles/genomicsdb-hts.dir/vcf.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/vcf.c -[ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o -MF CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o.d -o CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/vcfutils.c -[ 11%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_codecs.c -[ 11%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_decode.c -[ 11%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_encode.c -[ 12%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_index.c In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -2947,52 +2982,82 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 12%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o +[ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/textutils.c.o -MF CMakeFiles/genomicsdb-hts.dir/textutils.c.o.d -o CMakeFiles/genomicsdb-hts.dir/textutils.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/textutils.c +[ 11%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o -MF CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o.d -o CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/vcfutils.c +[ 12%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_codecs.c +[ 12%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_blosc.cc +[ 13%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_filter.cc +[ 13%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_decode.c +[ 13%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_filter_bit_shuffle.cc +[ 13%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_encode.c +[ 14%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_external.c +[ 14%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc +[ 14%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_index.c +[ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_gzip.cc +[ 15%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_io.c -[ 13%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o +[ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_lz4.cc +[ 16%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_samtools.c -[ 13%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o +[ 16%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_stats.c -[ 13%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc -[ 13%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o +[ 16%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_rle.cc +[ 17%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_zstd.cc +[ 17%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/mFILE.c -[ 14%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o +[ 18%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/open_trace_file.c -[ 14%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o +[ 18%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/pooled_alloc.c -[ 14%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o +[ 18%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -std=gnu11 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle/bitshuffle_core.c +[ 18%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/rANS_static.c -[ 14%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o +[ 18%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -std=gnu11 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle/iochain.c +[ 19%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/expressions/expression.cc +[ 19%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/book_keeping.cc +[ 19%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/fragment.cc +[ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/read_state.cc +[ 20%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/cram/string_alloc.c -[ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc -[ 15%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o +[ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/write_state.cc +[ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc +[ 20%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc -[ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec.cc -[ 15%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o +[ 20%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/variant_operations_columnar.cc -/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc: In function 'void TileDBUtils::print_md5_hash(unsigned char*, size_t)': -/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc:330:6: warning: 'unsigned char* TileDBUtils::MD5(const unsigned char*, size_t, unsigned char*)' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] - 330 | MD5(buffer, length, md); - | ~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc:327: -/usr/include/openssl/md5.h:52:38: note: declared here - 52 | OSSL_DEPRECATEDIN_3_0 unsigned char *MD5(const unsigned char *d, size_t n, - | ^~~ -[ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_blosc.cc -[ 16%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_filter.cc -[ 16%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_filter_bit_shuffle.cc -[ 16%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc -[ 17%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/broad_combined_gvcf_columnar.cc -[ 18%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_gzip.cc +[ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata_iterator.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -3015,10 +3080,25 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 18%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_lz4.cc -[ 18%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_rle.cc +[ 21%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/error.cc +[ 22%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/broad_combined_gvcf_columnar.cc +/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc: In member function 'int Metadata::read(const char*, void**, size_t*)': +/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc:105:6: warning: 'unsigned char* MD5(const unsigned char*, size_t, unsigned char*)' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] + 105 | MD5((const unsigned char*) key, strlen(key)+1, (unsigned char*) coords); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc:36: +/usr/include/openssl/md5.h:52:38: note: declared here + 52 | OSSL_DEPRECATEDIN_3_0 unsigned char *MD5(const unsigned char *d, size_t n, + | ^~~ +/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc: In member function 'void Metadata::compute_array_coords(const char*, size_t, void*&, size_t&) const': +/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc:418:8: warning: 'unsigned char* MD5(const unsigned char*, size_t, unsigned char*)' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] + 418 | MD5(keys_c, key_size, coords_c); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/openssl/md5.h:52:38: note: declared here + 52 | OSSL_DEPRECATEDIN_3_0 unsigned char *MD5(const unsigned char *d, size_t n, + | ^~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -3040,22 +3120,27 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 19%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_zstd.cc -[ 19%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -std=gnu11 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle/bitshuffle_core.c -[ 19%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -std=gnu11 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle/iochain.c -[ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/expressions/expression.cc -[ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/book_keeping.cc -[ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/fragment.cc -[ 21%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/read_state.cc -[ 21%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/write_state.cc +[ 22%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/hilbert_curve.cc +[ 22%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/mem_utils.cc +[ 23%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/progress_bar.cc +[ 23%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/uri.cc +[ 23%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/utils.cc +[ 24%] Linking C shared library libgenomicsdb-hts.so +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cmake -E cmake_link_script CMakeFiles/genomicsdb-hts.dir/link.txt --verbose=1 +/usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgenomicsdb-hts.so -o libgenomicsdb-hts.so "CMakeFiles/genomicsdb-hts.dir/kfunc.c.o" "CMakeFiles/genomicsdb-hts.dir/knetfile.c.o" "CMakeFiles/genomicsdb-hts.dir/kstring.c.o" "CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o" "CMakeFiles/genomicsdb-hts.dir/bgzf.c.o" "CMakeFiles/genomicsdb-hts.dir/errmod.c.o" "CMakeFiles/genomicsdb-hts.dir/faidx.c.o" "CMakeFiles/genomicsdb-hts.dir/header.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o" "CMakeFiles/genomicsdb-hts.dir/hts.c.o" "CMakeFiles/genomicsdb-hts.dir/hts_os.c.o" "CMakeFiles/genomicsdb-hts.dir/md5.c.o" "CMakeFiles/genomicsdb-hts.dir/multipart.c.o" "CMakeFiles/genomicsdb-hts.dir/probaln.c.o" "CMakeFiles/genomicsdb-hts.dir/realn.c.o" "CMakeFiles/genomicsdb-hts.dir/regidx.c.o" "CMakeFiles/genomicsdb-hts.dir/region.c.o" "CMakeFiles/genomicsdb-hts.dir/sam.c.o" "CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o" "CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o" "CMakeFiles/genomicsdb-hts.dir/tbx.c.o" "CMakeFiles/genomicsdb-hts.dir/textutils.c.o" "CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o" "CMakeFiles/genomicsdb-hts.dir/vcf.c.o" "CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o" /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/liblzma.so +[ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/storage_manager/storage_buffer.cc +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 25%] Built target genomicsdb-hts +[ 25%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc +[ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/storage_manager/storage_fs.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -3077,48 +3162,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc -[ 21%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata_iterator.cc -[ 22%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/error.cc -[ 22%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/hilbert_curve.cc -/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc: In member function 'int Metadata::read(const char*, void**, size_t*)': -/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc:105:6: warning: 'unsigned char* MD5(const unsigned char*, size_t, unsigned char*)' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] - 105 | MD5((const unsigned char*) key, strlen(key)+1, (unsigned char*) coords); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc:36: -/usr/include/openssl/md5.h:52:38: note: declared here - 52 | OSSL_DEPRECATEDIN_3_0 unsigned char *MD5(const unsigned char *d, size_t n, - | ^~~ -/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc: In member function 'void Metadata::compute_array_coords(const char*, size_t, void*&, size_t&) const': -/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc:418:8: warning: 'unsigned char* MD5(const unsigned char*, size_t, unsigned char*)' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] - 418 | MD5(keys_c, key_size, coords_c); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/openssl/md5.h:52:38: note: declared here - 52 | OSSL_DEPRECATEDIN_3_0 unsigned char *MD5(const unsigned char *d, size_t n, - | ^~~ -[ 22%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/mem_utils.cc -[ 23%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/progress_bar.cc -[ 24%] Linking C shared library libgenomicsdb-hts.so -[ 24%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cmake -E cmake_link_script CMakeFiles/genomicsdb-hts.dir/link.txt --verbose=1 -[ 24%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/uri.cc -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/utils.cc -/usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgenomicsdb-hts.so -o libgenomicsdb-hts.so "CMakeFiles/genomicsdb-hts.dir/kfunc.c.o" "CMakeFiles/genomicsdb-hts.dir/knetfile.c.o" "CMakeFiles/genomicsdb-hts.dir/kstring.c.o" "CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o" "CMakeFiles/genomicsdb-hts.dir/bgzf.c.o" "CMakeFiles/genomicsdb-hts.dir/errmod.c.o" "CMakeFiles/genomicsdb-hts.dir/faidx.c.o" "CMakeFiles/genomicsdb-hts.dir/header.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o" "CMakeFiles/genomicsdb-hts.dir/hts.c.o" "CMakeFiles/genomicsdb-hts.dir/hts_os.c.o" "CMakeFiles/genomicsdb-hts.dir/md5.c.o" "CMakeFiles/genomicsdb-hts.dir/multipart.c.o" "CMakeFiles/genomicsdb-hts.dir/probaln.c.o" "CMakeFiles/genomicsdb-hts.dir/realn.c.o" "CMakeFiles/genomicsdb-hts.dir/regidx.c.o" "CMakeFiles/genomicsdb-hts.dir/region.c.o" "CMakeFiles/genomicsdb-hts.dir/sam.c.o" "CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o" "CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o" "CMakeFiles/genomicsdb-hts.dir/tbx.c.o" "CMakeFiles/genomicsdb-hts.dir/textutils.c.o" "CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o" "CMakeFiles/genomicsdb-hts.dir/vcf.c.o" "CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o" /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/liblzma.so -[ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/storage_manager/storage_buffer.cc -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 25%] Built target genomicsdb-hts -[ 25%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc -[ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/storage_manager/storage_fs.cc [ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/storage_manager/storage_manager.cc [ 26%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o @@ -3127,8 +3170,17 @@ cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/storage_manager/storage_posixfs.cc [ 26%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -std=gnu11 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4/lz4.c +[ 26%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_cell.cc +[ 27%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_storage_manager.cc +[ 27%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_data.cc +[ 27%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc:25: + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, + from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_cell.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ @@ -3139,25 +3191,12 @@ from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, - from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/gt_remapper.h:26, - from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/gt_remapper_template_definition.h:25, - from /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc:23: + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 26%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_cell.cc -[ 26%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o -[ 27%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_data.cc -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_storage_manager.cc -[ 27%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc -[ 28%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_cell.cc:23: + from /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc:25: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ @@ -3168,7 +3207,9 @@ from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:26: + from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/gt_remapper.h:26, + from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/gt_remapper_template_definition.h:25, + from /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -3193,9 +3234,7 @@ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, - from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:23: + from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc:25: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ @@ -3206,8 +3245,8 @@ from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, - from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:27: + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_array_schema.h:27, + from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -3224,12 +3263,15 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 28%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc [ 28%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, - from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc:25: + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, + from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ @@ -3240,18 +3282,17 @@ from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_array_schema.h:27, - from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc:24: + from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 28%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/query_variants.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant.cc:23: + from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, + from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ @@ -3267,59 +3308,17 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 28%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/query_variants.cc [ 29%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_columnar_field.cc -/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc: In instantiation of 'bool VariantFieldHandler::concatenate_field(const Variant&, const VariantQueryConfig&, unsigned int, const void**, unsigned int&) [with DataType = std::__cxx11::basic_string; CombineResultType = std::__cxx11::basic_string]': -/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:973:16: required from here -/build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:56:54: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 56 | #define memcpy_s(dst, dst_size, src, src_size) memcpy((dst), (src), (src_size)) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:724:7: note: in expansion of macro 'memcpy_s' - 724 | memcpy_s(&(m_concatenation_result[curr_result_size]), vec.size()*sizeof(DataType), &(vec[0]), - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:53: -/usr/include/c++/12/bits/basic_string.h:85:11: note: '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} declared here - 85 | class basic_string - | ^~~~~~~~~~~~ -/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc: In instantiation of 'bool VariantFieldHandler::collect_and_extend_fields(const Variant&, const VariantQueryConfig&, unsigned int, const void**, uint64_t&, bool, bool, bool) [with DataType = std::__cxx11::basic_string; CombineResultType = std::__cxx11::basic_string; uint64_t = long unsigned int]': -/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:973:16: required from here -/build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:56:54: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 56 | #define memcpy_s(dst, dst_size, src, src_size) memcpy((dst), (src), (src_size)) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:797:7: note: in expansion of macro 'memcpy_s' - 797 | memcpy_s(&(m_extended_field_vector[extended_field_vector_idx]), field_ptr->length()*sizeof(DataType), - | ^~~~~~~~ -/usr/include/c++/12/bits/basic_string.h:85:11: note: '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} declared here - 85 | class basic_string - | ^~~~~~~~~~~~ -In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, - from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/query_variants.cc:24: -/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 290 | : std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, - from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, - from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/query_variants.cc:23: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 29%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_iterators.cc [ 29%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc [ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/loader/tiledb_loader_text_file.cc -In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_iterators.cc:24: +In file included from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_columnar_field.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ @@ -3330,11 +3329,17 @@ from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:26: + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_columnar_field.cc:23: +[ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/loader/load_operators.cc +In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, + from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/query_variants.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ @@ -3345,12 +3350,34 @@ from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:26: + from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, + from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/query_variants.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/loader/load_operators.cc +/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc: In instantiation of 'bool VariantFieldHandler::concatenate_field(const Variant&, const VariantQueryConfig&, unsigned int, const void**, unsigned int&) [with DataType = std::__cxx11::basic_string; CombineResultType = std::__cxx11::basic_string]': +/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:973:16: required from here +/build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:56:54: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 56 | #define memcpy_s(dst, dst_size, src, src_size) memcpy((dst), (src), (src_size)) + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:724:7: note: in expansion of macro 'memcpy_s' + 724 | memcpy_s(&(m_concatenation_result[curr_result_size]), vec.size()*sizeof(DataType), &(vec[0]), + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:53: +/usr/include/c++/12/bits/basic_string.h:85:11: note: '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} declared here + 85 | class basic_string + | ^~~~~~~~~~~~ +/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc: In instantiation of 'bool VariantFieldHandler::collect_and_extend_fields(const Variant&, const VariantQueryConfig&, unsigned int, const void**, uint64_t&, bool, bool, bool) [with DataType = std::__cxx11::basic_string; CombineResultType = std::__cxx11::basic_string; uint64_t = long unsigned int]': +/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:973:16: required from here +/build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:56:54: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 56 | #define memcpy_s(dst, dst_size, src, src_size) memcpy((dst), (src), (src_size)) + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:797:7: note: in expansion of macro 'memcpy_s' + 797 | memcpy_s(&(m_extended_field_vector[extended_field_vector_idx]), field_ptr->length()*sizeof(DataType), + | ^~~~~~~~ +/usr/include/c++/12/bits/basic_string.h:85:11: note: '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} declared here + 85 | class basic_string + | ^~~~~~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -3371,13 +3398,58 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/loader/genomicsdb_importer.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 30%] Built target TILEDB_CORE_OBJECTS make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 30%] Linking CXX static library libgenomicsdb-tiledb.a +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -P CMakeFiles/tiledb_static.dir/cmake_clean_target.cmake +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_static.dir/link.txt --verbose=1 +/usr/bin/ar qc libgenomicsdb-tiledb.a CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o +In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, + from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_iterators.cc:24: +/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 290 | : std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:26: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/usr/bin/ranlib libgenomicsdb-tiledb.a +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 30%] Built target tiledb_static +make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 31%] Linking CXX shared library libgenomicsdb-tiledb.so +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_shared.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgenomicsdb-tiledb.so -o libgenomicsdb-tiledb.so CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so +[ 31%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/loader/genomicsdb_importer.cc +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 31%] Built target tiledb_shared +make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 31%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o -MF CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o.d -o CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/array/test_array_schema.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -3399,9 +3471,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, @@ -3423,24 +3492,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Linking CXX static library libgenomicsdb-tiledb.a -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -P CMakeFiles/tiledb_static.dir/cmake_clean_target.cmake -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_static.dir/link.txt --verbose=1 -/usr/bin/ar qc libgenomicsdb-tiledb.a CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o -/usr/bin/ranlib libgenomicsdb-tiledb.a -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 30%] Built target tiledb_static -make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 31%] Linking CXX shared library libgenomicsdb-tiledb.so -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_shared.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgenomicsdb-tiledb.so -o libgenomicsdb-tiledb.so CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -[ 32%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/loader/tiledb_loader_file_base.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, @@ -3464,24 +3515,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 32%] Built target tiledb_shared -make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 32%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o -MF CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o.d -o CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/array/test_array_schema.cc +[ 32%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/loader/tiledb_loader_file_base.cc [ 32%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/loader/tiledb_loader.cc -[ 32%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/memory_measure.cc -[ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/histogram.cc -[ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/vid_mapper_pb.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, @@ -3504,23 +3541,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 32%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/memory_measure.cc +[ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/histogram.cc +[ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/vid_mapper_pb.cc [ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/lut.cc [ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/known_field_info.cc -make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 34%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -MF CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o.d -o CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/benchmark/test_print_array_schema.cc -[ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o +[ 34%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/vid_mapper.cc -[ 35%] Linking CXX executable test_print_array_schema -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_print_array_schema.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -o test_print_array_schema ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +[ 34%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/vid_mapper_sql.cc +[ 34%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/timer.cc +[ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/genomicsdb_logger.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -3543,30 +3581,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 35%] Built target test_print_array_schema -make -f genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 35%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o -MF CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o.d -o CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/benchmark/test_print_book_keeping.cc -[ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/vid_mapper_sql.cc -[ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/timer.cc -[ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/genomicsdb_logger.cc -[ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o +[ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc -[ 37%] Linking CXX executable test_print_book_keeping -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_print_book_keeping.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o -o test_print_book_keeping ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx -[ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/vcf_adapter.cc -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -3586,17 +3602,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 37%] Built target test_print_book_keeping -make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 38%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o -MF CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o.d -o CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/benchmark/test_sparse_array_benchmark.cc -[ 39%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o +[ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/vcf_adapter.cc +[ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/genomicsdb_bcf_generator.cc +[ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/vcf2binary.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -3637,8 +3648,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/vcf2binary.cc +[ 36%] Building C object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/cc -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/hfile_genomicsdb.c +[ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/htslib_fs_adapter.cc +[ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/config/variant_query_config.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -3659,18 +3674,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building C object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/cc -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/hfile_genomicsdb.c -[ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/htslib_fs_adapter.cc -[ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/config/variant_query_config.cc -[ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/config/genomicsdb_config_base.cc -[ 41%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/config/json_config.cc -[ 41%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/config/pb_config.cc /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/htslib_fs_adapter.cc: In function 'void* genomicsdb_filesystem_init(const char*, int)': /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/htslib_fs_adapter.cc:81:13: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'TileDB_Config' {aka 'struct TileDB_Config'}; use assignment or value-initialization instead [-Wclass-memaccess] 81 | memset(&tiledb_config, 0, sizeof(TileDB_Config)); @@ -3693,22 +3696,18 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 41%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o +[ 37%] Building CXX object 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-I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/config/genomicsdb_config_base.cc +[ 38%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 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-I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o -c /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_export_config.pb.cc -[ 44%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o -c /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_import_config.pb.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -3726,8 +3725,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 44%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o -c /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_vid_mapping.pb.cc +[ 39%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o -c /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc +[ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o -c /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_coordinates.pb.cc +[ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o -c /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_callsets_mapping.pb.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, @@ -3744,6 +3747,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o -c /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_export_config.pb.cc +[ 41%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o -c /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_import_config.pb.cc /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc: In member function 'virtual void GenomicsDBPlinkProcessor::process(const std::string&, const int64_t*, const genomic_interval_t&, const std::vector&, bool)': /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc:366:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 366 | if(g < 0 || g >= vec.size()) { @@ -3752,14 +3759,48 @@ /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc:653:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 653 | for(int i = 0; i < num_rows; i++) { | ~~^~~~~~~~~~ +[ 41%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o -c /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_vid_mapping.pb.cc +make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 42%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -MF CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o.d -o CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/benchmark/test_print_array_schema.cc +[ 42%] Linking CXX executable test_print_array_schema +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_print_array_schema.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -o test_print_array_schema ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +make -f genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 42%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o -MF CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o.d -o CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/benchmark/test_print_book_keeping.cc +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 42%] Built target test_print_array_schema +make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 43%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o -MF CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o.d -o CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/benchmark/test_sparse_array_benchmark.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o +[ 44%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o -MF CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o.d -o CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc +[ 45%] Linking CXX executable test_print_book_keeping +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_print_book_keeping.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o -o test_print_book_keeping ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/DependInfo.cmake --color= @@ -3776,6 +3817,8 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o -MF CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o.d -o CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/c_api/test_dense_array_api.cc +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 45%] Built target test_print_book_keeping make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/DependInfo.cmake --color= @@ -3819,14 +3862,14 @@ make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 46%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o -MF CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o.d -o CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_mem_utils.cc +make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' @@ -3840,13 +3883,18 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 47%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o -MF CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o.d -o CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc +[ 48%] Linking CXX executable test_array_schema +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_schema.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o -o test_array_schema ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 48%] Built target test_array_schema make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 47%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o +[ 48%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o -MF CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o.d -o CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/storage_manager/test_posixfs.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' @@ -3854,11 +3902,8 @@ make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 47%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o +[ 48%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o -MF CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o.d -o CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/storage_manager/test_storage_buffer.cc -[ 48%] Linking CXX executable test_array_schema -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_schema.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o -o test_array_schema ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx In file included from /usr/include/c++/12/string:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::push_back(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:1529:21, @@ -3874,7 +3919,7 @@ 606 | char p; | ^ make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 48%] Built target test_array_schema +[ 48%] Built target GenomicsDB_library_object_files make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/DependInfo.cmake --color= @@ -3905,28 +3950,28 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 50%] Built target GenomicsDB_library_object_files +[ 50%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o -MF CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o.d -o CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_consolidate.cc +[ 50%] Linking CXX executable tiledb_array_consolidate +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_consolidate.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o -o tiledb_array_consolidate ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 50%] Built target tiledb_array_consolidate make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/DependInfo.cmake --color= -[ 50%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o -MF CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o.d -o CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_consolidate.cc [ 51%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o -MF CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o.d -o CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_create_dense.cc -[ 51%] Linking CXX executable tiledb_array_consolidate -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_consolidate.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o -o tiledb_array_consolidate ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx [ 51%] Linking CXX executable tiledb_array_create_dense cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_create_dense.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o -o tiledb_array_create_dense ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 51%] Built target tiledb_array_consolidate +[ 51%] Built target tiledb_array_create_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/DependInfo.cmake --color= @@ -3939,7 +3984,7 @@ cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_create_sparse.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_create_sparse.dir/src/tiledb_array_create_sparse.cc.o -o tiledb_array_create_sparse ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 52%] Built target tiledb_array_create_dense +[ 52%] Built target tiledb_array_create_sparse make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/DependInfo.cmake --color= @@ -3950,9 +3995,9 @@ cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o -MF CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o.d -o CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_iterator_dense.cc [ 52%] Linking CXX executable tiledb_array_iterator_dense cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_iterator_dense.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o -o tiledb_array_iterator_dense ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 52%] Built target tiledb_array_create_sparse +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 52%] Built target tiledb_array_iterator_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/DependInfo.cmake --color= @@ -3965,7 +4010,7 @@ cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_iterator_sparse.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_iterator_sparse.dir/src/tiledb_array_iterator_sparse.cc.o -o tiledb_array_iterator_sparse ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 53%] Built target tiledb_array_iterator_dense +[ 53%] Built target tiledb_array_iterator_sparse make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/DependInfo.cmake --color= @@ -3978,7 +4023,7 @@ cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_iterator_sparse_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_iterator_sparse_filter.dir/src/tiledb_array_iterator_sparse_filter.cc.o -o tiledb_array_iterator_sparse_filter ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 54%] Built target tiledb_array_iterator_sparse +[ 54%] Built target tiledb_array_iterator_sparse_filter make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/DependInfo.cmake --color= @@ -3991,7 +4036,7 @@ cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o -o tiledb_array_parallel_consolidate_dense ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 54%] Built target tiledb_array_iterator_sparse_filter +[ 54%] Built target tiledb_array_parallel_consolidate_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/DependInfo.cmake --color= @@ -4000,8 +4045,11 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 55%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o -MF CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o.d -o CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_consolidate_sparse.cc +[ 55%] Linking CXX executable tiledb_array_parallel_consolidate_sparse +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o -o tiledb_array_parallel_consolidate_sparse ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 55%] Built target tiledb_array_parallel_consolidate_dense +[ 55%] Built target tiledb_array_parallel_consolidate_sparse make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/DependInfo.cmake --color= @@ -4010,14 +4058,11 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 55%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o -MF CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o.d -o CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_dense_1.cc -[ 55%] Linking CXX executable tiledb_array_parallel_consolidate_sparse -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o -o tiledb_array_parallel_consolidate_sparse ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx [ 56%] Linking CXX executable tiledb_array_parallel_read_dense_1 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_dense_1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o -o tiledb_array_parallel_read_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 56%] Built target tiledb_array_parallel_consolidate_sparse +[ 56%] Built target tiledb_array_parallel_read_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/DependInfo.cmake --color= @@ -4026,8 +4071,11 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 56%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o -MF CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o.d -o CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_dense_2.cc +[ 56%] Linking CXX executable tiledb_array_parallel_read_dense_2 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_dense_2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o -o tiledb_array_parallel_read_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 56%] Built target tiledb_array_parallel_read_dense_1 +[ 56%] Built target tiledb_array_parallel_read_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/DependInfo.cmake --color= @@ -4036,9 +4084,77 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 56%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o -MF CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o.d -o CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_mpi_io_dense.cc -[ 56%] Linking CXX executable tiledb_array_parallel_read_dense_2 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_dense_2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o -o tiledb_array_parallel_read_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +In file included from /usr/include/string.h:535, + from /usr/include/c++/12/cstring:42, + from /usr/include/catch2/catch.hpp:5717, + from /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2/catch.h:37, + from /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:38: +In function 'void* memcpy(void*, const void*, size_t)', + inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:183:11: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] + 29 | return __builtin___memcpy_chk (__dest, __src, __len, + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 30 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:10: note: source object 'j' of size 8 + 180 | double j = 0.1, k = 0.2; + | ^ +In function 'void* memcpy(void*, const void*, size_t)', + inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:185:11: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] + 29 | return __builtin___memcpy_chk (__dest, __src, __len, + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 30 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:19: note: source object 'k' of size 8 + 180 | double j = 0.1, k = 0.2; + | ^ +In function 'void* memcpy(void*, const void*, size_t)', + inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:190:11: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] + 29 | return __builtin___memcpy_chk (__dest, __src, __len, + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 30 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:10: note: source object 'j' of size 8 + 180 | double j = 0.1, k = 0.2; + | ^ +In function 'void* memcpy(void*, const void*, size_t)', + inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:191:11: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] + 29 | return __builtin___memcpy_chk (__dest, __src, __len, + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 30 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:19: note: source object 'k' of size 8 + 180 | double j = 0.1, k = 0.2; + | ^ +In function 'void* memcpy(void*, const void*, size_t)', + inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:195:11: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] + 29 | return __builtin___memcpy_chk (__dest, __src, __len, + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 30 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:10: note: source object 'j' of size 8 + 180 | double j = 0.1, k = 0.2; + | ^ +In function 'void* memcpy(void*, const void*, size_t)', + inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:197:11: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] + 29 | return __builtin___memcpy_chk (__dest, __src, __len, + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + 30 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': +/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:19: note: source object 'k' of size 8 + 180 | double j = 0.1, k = 0.2; + | ^ [ 57%] Linking CXX executable tiledb_array_parallel_read_mpi_io_dense cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o -o tiledb_array_parallel_read_mpi_io_dense ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx @@ -4050,10 +4166,13 @@ make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 57%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o -MF CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_sparse_1.cc -[ 57%] Built target tiledb_array_parallel_read_dense_2 +[ 57%] Linking CXX executable tiledb_array_parallel_read_sparse_1 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o -o tiledb_array_parallel_read_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 57%] Built target tiledb_array_parallel_read_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/DependInfo.cmake --color= @@ -4062,14 +4181,11 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 58%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o -MF CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o.d -o CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_sparse_2.cc -[ 58%] Linking CXX executable tiledb_array_parallel_read_sparse_1 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o -o tiledb_array_parallel_read_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx [ 58%] Linking CXX executable tiledb_array_parallel_read_sparse_2 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o -o tiledb_array_parallel_read_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 58%] Built target tiledb_array_parallel_read_sparse_1 +[ 58%] Built target tiledb_array_parallel_read_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/DependInfo.cmake --color= @@ -4078,24 +4194,24 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 58%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o -MF CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o.d -o CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_dense_1.cc +[ 59%] Linking CXX executable tiledb_array_parallel_write_dense_1 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_dense_1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o -o tiledb_array_parallel_write_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 58%] Built target tiledb_array_parallel_read_sparse_2 +[ 59%] Built target tiledb_array_parallel_write_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 58%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o +[ 59%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o -MF CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o.d -o CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_dense_2.cc -[ 59%] Linking CXX executable tiledb_array_parallel_write_dense_1 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_dense_1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o -o tiledb_array_parallel_write_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx [ 59%] Linking CXX executable tiledb_array_parallel_write_dense_2 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_dense_2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o -o tiledb_array_parallel_write_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 59%] Built target tiledb_array_parallel_write_dense_1 +[ 59%] Built target tiledb_array_parallel_write_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/DependInfo.cmake --color= @@ -4104,8 +4220,11 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 60%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o -MF CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_sparse_1.cc +[ 60%] Linking CXX executable tiledb_array_parallel_write_sparse_1 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o -o tiledb_array_parallel_write_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 60%] Built target tiledb_array_parallel_write_dense_2 +[ 60%] Built target tiledb_array_parallel_write_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/DependInfo.cmake --color= @@ -4114,66 +4233,68 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 60%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o -MF CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o.d -o CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_sparse_2.cc -[ 60%] Linking CXX executable tiledb_array_parallel_write_sparse_1 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o -o tiledb_array_parallel_write_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx [ 61%] Linking CXX executable tiledb_array_parallel_write_sparse_2 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o -o tiledb_array_parallel_write_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 61%] Built target tiledb_array_parallel_write_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/depend -[ 61%] Built target tiledb_array_parallel_write_sparse_1 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 61%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o -MF CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o.d -o CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_primitive.cc +[ 61%] Linking CXX executable tiledb_array_primitive +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_primitive.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o -o tiledb_array_primitive ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 61%] Built target tiledb_array_primitive make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 61%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o -MF CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o.d -o CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_primitive.cc [ 62%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o -MF CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o.d -o CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_1.cc -[ 62%] Linking CXX executable tiledb_array_primitive -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_primitive.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o -o tiledb_array_primitive ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 62%] Linking CXX executable tiledb_array_read_dense_1 +[ 62%] Linking CXX executable test_array_iterator +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_iterator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o -o test_array_iterator ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +/usr/bin/ld: [ 62%] Linking CXX executable tiledb_array_read_dense_1 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o -o tiledb_array_read_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o: in function `TempDir::create_temp_directory()': +./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 62%] Built target tiledb_array_primitive +[ 62%] Built target tiledb_array_read_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 62%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o -MF CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o.d -o CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_2.cc -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 62%] Built target tiledb_array_read_dense_1 +[ 62%] Built target test_array_iterator make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/DependInfo.cmake --color= +[ 62%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o -MF CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o.d -o CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_2.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 62%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o -MF CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o.d -o CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_3.cc [ 63%] Linking CXX executable tiledb_array_read_dense_2 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_2.dir/link.txt --verbose=1 -[ 63%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o -MF CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o.d -o CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_3.cc -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o -o tiledb_array_read_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx [ 63%] Linking CXX executable tiledb_array_read_dense_3 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o -o tiledb_array_read_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o -o tiledb_array_read_dense_3 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 63%] Built target tiledb_array_read_dense_2 +[ 63%] Built target tiledb_array_read_dense_3 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/DependInfo.cmake --color= @@ -4182,111 +4303,35 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 63%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o -MF CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o.d -o CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_sorted.cc -In file included from /usr/include/string.h:535, - from /usr/include/c++/12/cstring:42, - from /usr/include/catch2/catch.hpp:5717, - from /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2/catch.h:37, - from /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:38: -In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:183:11: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] - 29 | return __builtin___memcpy_chk (__dest, __src, __len, - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - 30 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:10: note: source object 'j' of size 8 - 180 | double j = 0.1, k = 0.2; - | ^ -In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:185:11: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] - 29 | return __builtin___memcpy_chk (__dest, __src, __len, - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - 30 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:19: note: source object 'k' of size 8 - 180 | double j = 0.1, k = 0.2; - | ^ -In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:190:11: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] - 29 | return __builtin___memcpy_chk (__dest, __src, __len, - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - 30 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:10: note: source object 'j' of size 8 - 180 | double j = 0.1, k = 0.2; - | ^ -In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:191:11: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] - 29 | return __builtin___memcpy_chk (__dest, __src, __len, - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - 30 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:19: note: source object 'k' of size 8 - 180 | double j = 0.1, k = 0.2; - | ^ -In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:195:11: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] - 29 | return __builtin___memcpy_chk (__dest, __src, __len, - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - 30 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:10: note: source object 'j' of size 8 - 180 | double j = 0.1, k = 0.2; - | ^ -In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:197:11: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] - 29 | return __builtin___memcpy_chk (__dest, __src, __len, - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ - 30 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': -/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:19: note: source object 'k' of size 8 - 180 | double j = 0.1, k = 0.2; - | ^ -[ 64%] Linking CXX executable tiledb_array_read_dense_sorted -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_sorted.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o -o tiledb_array_read_dense_sorted ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 64%] Linking CXX executable test_sparse_array_benchmark -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sparse_array_benchmark.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o -o test_sparse_array_benchmark ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 64%] Built target tiledb_array_read_dense_3 +[ 63%] Built target tiledb_array_read_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 64%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o +[ 63%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o -MF CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_1.cc +[ 64%] Linking CXX executable tiledb_array_read_dense_sorted +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_sorted.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o -o tiledb_array_read_dense_sorted ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 64%] Linking CXX executable tiledb_array_read_sparse_1 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o -o tiledb_array_read_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 64%] Linking CXX executable test_tiledb_utils +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tiledb_utils.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o -o test_tiledb_utils ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx /usr/bin/ld: make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 64%] Built target tiledb_array_read_dense_sorted make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/DependInfo.cmake --color= -[ 64%] Linking CXX executable tiledb_array_read_sparse_1 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_1.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 65%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o -o tiledb_array_read_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o -MF CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o.d -o CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_2.cc -CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o: in function `TempDir::create_temp_directory()': -./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -[ 65%] Linking CXX executable tiledb_array_read_sparse_2 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o -o tiledb_array_read_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 65%] Built target tiledb_array_read_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/depend @@ -4295,10 +4340,15 @@ make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o: in function `TempDir::create_temp_directory()': +./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' [ 65%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o -MF CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o.d -o CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_filter_1.cc +[ 65%] Linking CXX executable tiledb_array_read_sparse_2 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o -o tiledb_array_read_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 65%] Built target tiledb_array_read_sparse_2 +[ 65%] Built target test_tiledb_utils make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/DependInfo.cmake --color= @@ -4307,26 +4357,34 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 65%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o -MF CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o.d -o CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_filter_2.cc +[ 65%] Linking CXX executable test_sparse_array_benchmark [ 66%] Linking CXX executable tiledb_array_read_sparse_filter_1 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_filter_1.dir/link.txt --verbose=1 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sparse_array_benchmark.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o -o tiledb_array_read_sparse_filter_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o -o test_sparse_array_benchmark ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +[ 66%] Linking CXX executable test_codec +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_codec.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o -o test_codec ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 66%] Linking CXX executable tiledb_array_read_sparse_filter_2 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_filter_2.dir/link.txt --verbose=1 -[ 66%] Built target test_sparse_array_benchmark +[ 66%] Built target tiledb_array_read_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o -o tiledb_array_read_sparse_filter_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 66%] Linking CXX executable tiledb_array_read_sparse_filter_2 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_filter_2.dir/link.txt --verbose=1 [ 67%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o -MF CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o.d -o CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_sorted.cc -[ 67%] Linking CXX executable tiledb_array_read_sparse_sorted +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o -o tiledb_array_read_sparse_filter_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +/usr/bin/ld: [ 67%] Linking CXX executable tiledb_array_read_sparse_sorted cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_sorted.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o -o tiledb_array_read_sparse_sorted ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o: in function `TempDir::create_temp_directory()': +./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 67%] Built target tiledb_array_read_sparse_filter_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' @@ -4334,67 +4392,67 @@ make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 67%] Linking CXX executable test_dense_array_api [ 67%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o -MF CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o.d -o CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_update_dense_1.cc +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_dense_array_api.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o -o test_dense_array_api ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 67%] Built target tiledb_array_read_sparse_filter_2 +[ 67%] Built target test_codec make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/DependInfo.cmake --color= -[ 68%] Linking CXX executable tiledb_array_update_dense_1 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_dense_1.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o -o tiledb_array_update_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 68%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o +[ 67%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o -MF CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o.d -o CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_update_dense_2.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 68%] Built target tiledb_array_read_sparse_sorted +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 67%] Built target tiledb_array_read_sparse_filter_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 69%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -MF CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_update_sparse_1.cc -[ 69%] Linking CXX executable tiledb_array_update_dense_2 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_dense_2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o -o tiledb_array_update_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 69%] Linking CXX executable test_array_iterator -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_iterator.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o -o test_array_iterator ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx -[ 69%] Built target tiledb_array_update_dense_1 +[ 67%] Built target tiledb_array_read_sparse_sorted make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/DependInfo.cmake --color= -[ 69%] Linking CXX executable tiledb_array_update_sparse_1 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_sparse_1.dir/link.txt --verbose=1 +/usr/bin/ld: make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -o tiledb_array_update_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 69%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o +[ 68%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -MF CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_update_sparse_1.cc +[ 68%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o -MF CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o.d -o CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_update_sparse_2.cc -/usr/bin/ld: make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 69%] Linking CXX executable tiledb_array_update_dense_1 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_dense_1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o -o tiledb_array_update_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o: in function `TempDir::create_temp_directory()': +./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' +[ 69%] Linking CXX executable tiledb_array_update_dense_2 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_dense_2.dir/link.txt --verbose=1 [ 70%] Linking CXX executable tiledb_array_update_sparse_2 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_sparse_2.dir/link.txt --verbose=1 -[ 70%] Built target tiledb_array_update_dense_2 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/depend +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o -o tiledb_array_update_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o -o tiledb_array_update_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 70%] Built target test_sparse_array_benchmark +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o: in function `TempDir::create_temp_directory()': -./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' [ 70%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o -MF CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o.d -o CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_1.cc +[ 70%] Linking CXX executable tiledb_array_update_sparse_1 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_sparse_1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -o tiledb_array_update_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 70%] Built target tiledb_array_update_sparse_1 +[ 70%] Built target test_dense_array_api make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/DependInfo.cmake --color= @@ -4404,8 +4462,11 @@ [ 71%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o -MF CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o.d -o CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_2.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 71%] Built target tiledb_array_update_sparse_2 +[ 71%] Linking CXX executable test_array_schema_api +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_schema_api.dir/link.txt --verbose=1 +[ 71%] Built target tiledb_array_update_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/depend +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o -o test_array_schema_api ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' @@ -4414,397 +4475,385 @@ [ 71%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o -MF CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o.d -o CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_sorted.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 71%] Built target test_array_iterator +[ 71%] Linking CXX executable tiledb_array_write_dense_1 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_dense_1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o -o tiledb_array_write_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 71%] Built target tiledb_array_update_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/DependInfo.cmake --color= -[ 71%] Linking CXX executable tiledb_array_write_dense_1 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_dense_1.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 72%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o +/usr/bin/ld: [ 72%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o -MF CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_1.cc -[ 72%] Linking CXX executable tiledb_array_write_dense_2 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_dense_2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o -o tiledb_array_write_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o -o tiledb_array_write_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 72%] Linking CXX executable tiledb_array_write_dense_sorted -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_dense_sorted.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o -o tiledb_array_write_dense_sorted ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 73%] Linking CXX executable test_mem_utils +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mem_utils.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o -o test_mem_utils ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 72%] Linking CXX executable tiledb_array_write_sparse_1 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_1.dir/link.txt --verbose=1 -[ 72%] Built target tiledb_array_write_dense_2 +[ 73%] Built target tiledb_array_update_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o -o tiledb_array_write_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o -MF CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o.d -o CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_2.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 72%] Built target tiledb_array_write_dense_1 -[ 72%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o +[ 73%] Built target tiledb_array_update_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/DependInfo.cmake --color= -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o -MF CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o.d -o CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_2.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 72%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o +[ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o -MF CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o.d -o CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_3.cc -[ 72%] Linking CXX executable test_codec -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_codec.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o -o test_codec ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx -[ 72%] Linking CXX executable tiledb_array_write_sparse_3 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_3.dir/link.txt --verbose=1 -[ 73%] Linking CXX executable tiledb_array_write_sparse_2 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o -o tiledb_array_write_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o -o tiledb_array_write_sparse_3 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o: in function `TempDir::create_temp_directory()': +./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' +[ 73%] Linking CXX executable tiledb_array_write_dense_2 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_dense_2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o -o tiledb_array_write_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 73%] Linking CXX executable tiledb_array_write_dense_sorted +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_dense_sorted.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o -o tiledb_array_write_dense_sorted ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 74%] Linking CXX executable test_codec_filter +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_codec_filter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o -o test_codec_filter ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +[ 74%] Linking CXX executable test_uri +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_uri.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 73%] Built target tiledb_array_write_sparse_1 +[ 74%] Built target test_mem_utils make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_uri.dir/src/misc/test_uri.cc.o -o test_uri ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 74%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o +[ 75%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o -MF CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o.d -o CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_4.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 74%] Built target tiledb_array_write_dense_sorted +[ 76%] Linking CXX executable tiledb_array_write_sparse_2 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_2.dir/link.txt --verbose=1 +[ 76%] Built target tiledb_array_write_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o -o tiledb_array_write_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 74%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o +[ 76%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o -MF CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o.d -o CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_catching_errors.cc +[ 76%] Linking CXX executable tiledb_array_write_sparse_1 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_1.dir/link.txt --verbose=1 +[ 76%] Linking CXX executable tiledb_array_write_sparse_3 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o -o tiledb_array_write_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o -o tiledb_array_write_sparse_3 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 74%] Built target test_codec +[ 76%] Built target test_codec_filter make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/DependInfo.cmake --color= -[ 74%] Linking CXX executable tiledb_array_write_sparse_4 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_4.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o -o tiledb_array_write_sparse_4 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 74%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o -MF CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o.d -o CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_clear_delete_move.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 74%] Built target tiledb_array_write_sparse_2 +[ 76%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o -MF CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o.d -o CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_clear_delete_move.cc +[ 76%] Built target test_array_schema_api make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 75%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o +[ 77%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o -MF CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o.d -o CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_config.cc -[ 76%] Linking CXX executable tiledb_catching_errors -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_catching_errors.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o -o tiledb_catching_errors ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 76%] Built target tiledb_array_write_sparse_3 +[ 77%] Built target tiledb_array_write_dense_sorted make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/depend +[ 77%] Built target test_uri +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/depend +[ 77%] Built target tiledb_array_write_dense_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 76%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o -MF CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o.d -o CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_delete.cc -[ 76%] Linking CXX executable tiledb_config -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_config.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o -o tiledb_config ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 76%] Linking CXX executable tiledb_clear_delete_move -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_clear_delete_move.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o -o tiledb_clear_delete_move ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 76%] Built target tiledb_array_write_sparse_4 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/depend +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 76%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o -MF CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o.d -o CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_ls.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 76%] Built target tiledb_catching_errors -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/depend +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build +[ 77%] Linking CXX executable tiledb_array_write_sparse_4 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/DependInfo.cmake --color= +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_4.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build +[ 77%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o -MF CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o.d -o CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_delete.cc make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 76%] Linking CXX executable tiledb_ls -[ 77%] Linking CXX executable tiledb_delete -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_ls.dir/link.txt --verbose=1 -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_delete.dir/link.txt --verbose=1 +[ 77%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o -o tiledb_array_write_sparse_4 ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o -MF CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o.d -o CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_ls.cc [ 78%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o -MF CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o.d -o CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_ls_workspaces.cc -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o -o tiledb_delete ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o -o tiledb_ls ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 79%] Linking CXX executable tiledb_catching_errors +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_catching_errors.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o -o tiledb_catching_errors ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 78%] Built target tiledb_clear_delete_move +[ 79%] Built target tiledb_array_write_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 78%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o +[ 79%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o -MF CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o.d -o CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_consolidate.cc -[ 78%] Built target tiledb_config +[ 79%] Linking CXX executable tiledb_config +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_config.dir/link.txt --verbose=1 +[ 79%] Linking CXX executable tiledb_clear_delete_move +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_clear_delete_move.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o -o tiledb_config ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o -o tiledb_clear_delete_move ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 79%] Built target tiledb_array_write_sparse_3 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 78%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o -MF CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o.d -o CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_create.cc -[ 79%] Linking CXX executable tiledb_metadata_consolidate -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_consolidate.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o -o tiledb_metadata_consolidate ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 79%] Linking CXX executable tiledb_ls_workspaces -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_ls_workspaces.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o -o tiledb_ls_workspaces ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 79%] Linking CXX executable tiledb_metadata_create -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_create.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o -o tiledb_metadata_create ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 79%] Built target tiledb_delete +[ 79%] Built target tiledb_array_write_sparse_4 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/DependInfo.cmake --color= +[ 79%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o -MF CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o.d -o CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_create.cc +[ 79%] Linking CXX executable tiledb_ls_workspaces +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_ls_workspaces.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 79%] Linking CXX executable tiledb_ls +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_ls.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o -o tiledb_ls ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx [ 79%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o -MF CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o.d -o CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_iterator.cc +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o -o tiledb_ls_workspaces ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 79%] Built target tiledb_ls_workspaces +[ 79%] Built target tiledb_array_write_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/DependInfo.cmake --color= -[ 79%] Built target tiledb_metadata_consolidate -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 79%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o -MF CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o.d -o CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_primitive.cc -[ 80%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -MF CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o.d -o CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_read.cc -[ 81%] Linking CXX executable tiledb_metadata_iterator +[ 80%] Linking CXX executable tiledb_metadata_consolidate +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_consolidate.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o -o tiledb_metadata_consolidate ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 81%] Linking CXX executable tiledb_delete +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_delete.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o -o tiledb_delete ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 82%] Linking CXX executable tiledb_metadata_iterator cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_iterator.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o -o tiledb_metadata_iterator ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 81%] Linking CXX executable tiledb_metadata_read -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_read.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -o tiledb_metadata_read ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -[ 81%] Linking CXX executable tiledb_metadata_primitive +[ 82%] Built target tiledb_catching_errors +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 83%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -MF CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o.d -o CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_read.cc +[ 83%] Linking CXX executable tiledb_metadata_primitive cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_primitive.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o -o tiledb_metadata_primitive ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 83%] Linking CXX executable tiledb_metadata_create +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_create.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 81%] Built target tiledb_metadata_create +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o -o tiledb_metadata_create ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 83%] Built target tiledb_config make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 81%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o -MF CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o.d -o CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_update.cc -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 81%] Built target tiledb_metadata_iterator +[ 83%] Built target tiledb_clear_delete_move make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/depend +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 83%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o -MF CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o.d -o CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_update.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 81%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o +[ 83%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o -MF CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o.d -o CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_write.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 81%] Built target tiledb_ls +[ 83%] Built target tiledb_metadata_consolidate make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 81%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o -MF CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o.d -o CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_workspace_group_create.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 81%] Built target tiledb_metadata_read +[ 83%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o +[ 83%] Built target tiledb_ls +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o -MF CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o.d -o CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_workspace_group_create.cc make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/tiledbgenomicsdb.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 81%] Linking CXX shared library libgenomicsdb.so -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledbgenomicsdb.dir/link.txt --verbose=1 -[ 81%] Linking CXX executable tiledb_metadata_write -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_write.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -shared -Wl,-soname,libgenomicsdb.so.0 -o libgenomicsdb.so.1.4.4 CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core: /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl ../../genomicsdb-htslib/libgenomicsdb-hts.so ../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/liblzma.so -[ 82%] Linking CXX executable tiledb_metadata_update -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o -o tiledb_metadata_write ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_update.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat 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Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdb.dir/DependInfo.cmake --color= +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -shared -Wl,-soname,libgenomicsdb.so.0 -o libgenomicsdb.so.1.4.4 CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o 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/usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/liblzma.so make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 83%] Linking CXX static library libgenomicsdb.a +[ 84%] Linking CXX static library libgenomicsdb.a cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/cmake -P CMakeFiles/genomicsdb.dir/cmake_clean_target.cmake cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/genomicsdb.dir/link.txt --verbose=1 /usr/bin/ar qc libgenomicsdb.a 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CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o -[ 83%] Linking CXX executable test_dense_array_api -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_dense_array_api.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o -o test_dense_array_api ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx -[ 84%] Linking CXX executable tiledb_workspace_group_create +[ 84%] Linking CXX executable tiledb_metadata_read +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_read.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -o tiledb_metadata_read ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +[ 84%] Linking CXX executable tiledb_metadata_write +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_write.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o -o tiledb_metadata_write ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 84%] Built target tiledb_delete +[ 84%] Built target tiledb_metadata_iterator +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 84%] Built target tiledb_metadata_primitive +[ 85%] Linking CXX executable tiledb_metadata_update +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_update.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 85%] Built target tiledb_metadata_create +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o -o tiledb_metadata_update ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 85%] Built target tiledb_metadata_read +[ 86%] Linking CXX executable tiledb_workspace_group_create cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_workspace_group_create.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o -o tiledb_workspace_group_create ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 84%] Built target tiledb_metadata_write -/usr/bin/ld: make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 84%] Built target tiledb_metadata_update make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 84%] Built target tiledb_workspace_group_create -CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o: in function `TempDir::create_temp_directory()': -./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -[ 85%] Linking CXX executable test_codec_filter -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_codec_filter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o -o test_codec_filter ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +[ 86%] Built target tiledb_metadata_write +[ 86%] Built target tiledb_metadata_update /usr/bin/ranlib libgenomicsdb.a make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 86%] Built target tiledb_workspace_group_create make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 85%] Built target test_codec_filter -[ 85%] Built target test_dense_array_api -[ 85%] Linking CXX executable test_array_schema_api -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_schema_api.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o -o test_array_schema_api ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx -[ 85%] Linking CXX executable test_tiledb_utils -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tiledb_utils.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o -o test_tiledb_utils ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx -/usr/bin/ld: /usr/bin/ld: CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o: in function `TempDir::create_temp_directory()': -./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o: in function `TempDir::create_temp_directory()': -./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -[ 85%] Built target genomicsdb +[ 86%] Built target genomicsdb make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f src/test/cpp/CMakeFiles/api_tests.dir/build.make src/test/cpp/CMakeFiles/api_tests.dir/depend +make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp 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/build/genomicsdb-1.4.4/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/DependInfo.cmake --color= make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/gt_mpi_gather.dir/DependInfo.cmake --color= make -f tools/CMakeFiles/vcf2genomicsdb.dir/build.make tools/CMakeFiles/vcf2genomicsdb.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb_init.dir/DependInfo.cmake --color= +make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f src/test/cpp/CMakeFiles/api_tests.dir/build.make src/test/cpp/CMakeFiles/api_tests.dir/build +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f tools/CMakeFiles/gt_mpi_gather.dir/build.make tools/CMakeFiles/gt_mpi_gather.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f tools/CMakeFiles/gt_mpi_gather.dir/build.make tools/CMakeFiles/gt_mpi_gather.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 86%] Building CXX object src/test/cpp/CMakeFiles/api_tests.dir/src/ctest_main.cc.o make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/build -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/api_tests.dir/src/ctest_main.cc.o -MF CMakeFiles/api_tests.dir/src/ctest_main.cc.o.d -o CMakeFiles/api_tests.dir/src/ctest_main.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/ctest_main.cc -make -f tools/CMakeFiles/vcf2genomicsdb.dir/build.make tools/CMakeFiles/vcf2genomicsdb.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 86%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/ctest_main.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/ctest_main.cc.o -MF CMakeFiles/ctests.dir/src/ctest_main.cc.o.d -o CMakeFiles/ctests.dir/src/ctest_main.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/ctest_main.cc -[ 86%] Building CXX object tools/CMakeFiles/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o -[ 86%] Building CXX object tools/CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader 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-Wno-unused-result -fopenmp -fPIE -MD -MT tools/CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o -MF CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o.d -o CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o -c /build/genomicsdb-1.4.4/tools/src/vcf2genomicsdb.cc cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/tools/include -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT tools/CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o -MF CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o.d -o CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o -c /build/genomicsdb-1.4.4/tools/src/vcfdiff.cc +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/cmake -E cmake_symlink_library libgenomicsdb.so.1.4.4 libgenomicsdb.so.0 libgenomicsdb.so make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 86%] Built target test_array_schema_api +[ 87%] Built target tiledbgenomicsdb make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf_histogram.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 87%] Building CXX object tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o +[ 88%] Building CXX object tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/tools/include -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o -MF CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o.d -o CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o -c /build/genomicsdb-1.4.4/tools/src/vcf_histogram.cc -[ 88%] Linking CXX executable create_genomicsdb_workspace +[ 89%] Linking CXX executable create_genomicsdb_workspace cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/create_genomicsdb_workspace.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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/usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 88%] Built target create_genomicsdb_workspace +[ 89%] Built target create_genomicsdb_workspace make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 89%] Building CXX object tools/CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o +[ 90%] Building CXX object tools/CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/tools/include -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT tools/CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o -MF CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o.d -o CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o -c /build/genomicsdb-1.4.4/tools/src/consolidate_genomicsdb_array.cc -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/cmake -E cmake_symlink_library libgenomicsdb.so.1.4.4 libgenomicsdb.so.0 libgenomicsdb.so -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 89%] Built target tiledbgenomicsdb -make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 89%] Building CXX object example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o -MF CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o.d -o CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o -c /build/genomicsdb-1.4.4/example/src/test_genomicsdb_bcf_generator.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -4842,6 +4891,11 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 90%] Linking CXX executable test_utils +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_utils.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o -o test_utils ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +/usr/bin/ld: CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o: in function `TempDir::create_temp_directory()': +./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, @@ -4866,12 +4920,11 @@ | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, - from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, - from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:27, - from /build/genomicsdb-1.4.4/example/src/test_genomicsdb_bcf_generator.cc:25: + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, + from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:27, + from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:29, + from /build/genomicsdb-1.4.4/tools/src/vcf_histogram.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ @@ -4882,17 +4935,28 @@ from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, - from /build/genomicsdb-1.4.4/example/src/test_genomicsdb_bcf_generator.cc:24: + from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/vcf2binary.h:26, + from /build/genomicsdb-1.4.4/tools/src/vcf_histogram.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 90%] Built target test_utils +make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 90%] Building CXX object example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o -MF CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o.d -o CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o -c /build/genomicsdb-1.4.4/example/src/test_genomicsdb_bcf_generator.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:29, - from /build/genomicsdb-1.4.4/tools/src/vcf_histogram.cc:24: + from /build/genomicsdb-1.4.4/tools/src/consolidate_genomicsdb_array.cc:28: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ @@ -4902,19 +4966,23 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, - from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/vcf2binary.h:26, - from /build/genomicsdb-1.4.4/tools/src/vcf_histogram.cc:23: + from /build/genomicsdb-1.4.4/tools/src/consolidate_genomicsdb_array.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc:28: +/build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc: In member function 'virtual void OneQueryIntervalProcessor::process(const std::string&, const int64_t*, const genomic_interval_t&, const std::vector&)': +/build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc:296:37: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 296 | CHECK(genomic_fields.size() == m_attributes_size + 2); // Add '2' for REF and ALT fields + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, - from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:27, - from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:29, - from /build/genomicsdb-1.4.4/tools/src/consolidate_genomicsdb_array.cc:28: + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, + from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, + from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, + from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:27, + from /build/genomicsdb-1.4.4/example/src/test_genomicsdb_bcf_generator.cc:25: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ @@ -4924,45 +4992,77 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from /build/genomicsdb-1.4.4/tools/src/consolidate_genomicsdb_array.cc:25: + from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, + from /build/genomicsdb-1.4.4/example/src/test_genomicsdb_bcf_generator.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 90%] Linking CXX executable test_mem_utils -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mem_utils.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o -o test_mem_utils ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +/build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc: In function 'void C_A_T_C_H_T_E_S_T_40()': +/build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc:589:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 589 | CHECK(num_threads == threads.size()); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +[ 90%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o -MF CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o.d -o CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_non_diploid_mapper.cc +[ 90%] Linking CXX executable test_sparse_array_api +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sparse_array_api.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o -o test_sparse_array_api ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +/usr/bin/ld: CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o: in function `TempDir::create_temp_directory()': +./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 90%] Built target test_mem_utils +[ 90%] Built target test_sparse_array_api make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/DependInfo.cmake --color= -[ 90%] Linking CXX executable test_uri -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_uri.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/build -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_uri.dir/src/misc/test_uri.cc.o -o test_uri ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, + from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, + from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, + from /build/genomicsdb-1.4.4/src/test/cpp/src/test_non_diploid_mapper.cc:26: +/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 290 | : std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/12/string:45, + from /usr/include/catch2/catch.hpp:477, + from /build/genomicsdb-1.4.4/src/test/cpp/src/test_non_diploid_mapper.cc:24: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ [ 91%] Building CXX object example/CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT example/CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o -MF CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o.d -o CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o -c /build/genomicsdb-1.4.4/example/src/test_genomicsdb_importer.cc -[ 91%] Linking CXX executable test_utils -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_utils.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o -o test_utils ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +[ 92%] Linking CXX executable test_storage_buffer +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_storage_buffer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o -o test_storage_buffer ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +/usr/bin/ld: CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o: in function `TempDir::create_temp_directory()': +./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' +[ 92%] Linking CXX executable test_genomicsdb_bcf_generator +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_genomicsdb_bcf_generator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o -o test_genomicsdb_bcf_generator -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl +[ 92%] Linking CXX executable test_posixfs +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_posixfs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o -o test_posixfs ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 91%] Built target test_uri +[ 92%] Built target test_storage_buffer make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 91%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o +[ 92%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o -c /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBUtils.cc -/usr/bin/ld: CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o: in function `TempDir::create_temp_directory()': +/usr/bin/ld: CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o: in function `TempDir::create_temp_directory()': ./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 91%] Built target test_utils -[ 91%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o +[ 92%] Built target test_posixfs +[ 92%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o -c /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc +[ 92%] Linking CXX executable gt_mpi_gather +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/gt_mpi_gather.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o -o gt_mpi_gather -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, @@ -4977,9 +5077,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 91%] Linking CXX executable test_genomicsdb_bcf_generator -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_genomicsdb_bcf_generator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o -o test_genomicsdb_bcf_generator -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 92%] Built target test_genomicsdb_bcf_generator +[ 93%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o -c /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBQuery.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, @@ -5002,9 +5103,19 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 91%] Linking CXX executable gt_mpi_gather -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/gt_mpi_gather.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o -o gt_mpi_gather -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl +[ 94%] Linking CXX executable vcfdiff +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdiff.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o -o vcfdiff -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 94%] Built target gt_mpi_gather +[ 94%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o -c /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBQueryStream.cc +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 94%] Built target vcfdiff +[ 95%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_multid_vector.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_multid_vector.cc.o -MF CMakeFiles/ctests.dir/src/test_multid_vector.cc.o.d -o CMakeFiles/ctests.dir/src/test_multid_vector.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_multid_vector.cc +[ 95%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o -c /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_jni_init.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, @@ -5027,33 +5138,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 91%] Built target test_genomicsdb_bcf_generator -[ 91%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_config.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_config.cc.o -MF CMakeFiles/ctests.dir/src/test_config.cc.o.d -o CMakeFiles/ctests.dir/src/test_config.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_config.cc -[ 92%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o -c /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBQuery.cc -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 92%] Built target gt_mpi_gather -[ 92%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o -MF CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o.d -o CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_non_diploid_mapper.cc -[ 92%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o -c /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBQueryStream.cc -In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, - from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, - from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, - from /build/genomicsdb-1.4.4/src/test/cpp/src/test_non_diploid_mapper.cc:26: -/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 290 | : std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/12/string:45, - from /usr/include/catch2/catch.hpp:477, - from /build/genomicsdb-1.4.4/src/test/cpp/src/test_non_diploid_mapper.cc:24: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 95%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_pb.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_pb.cc.o -MF CMakeFiles/ctests.dir/src/test_pb.cc.o.d -o CMakeFiles/ctests.dir/src/test_pb.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_pb.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -5076,26 +5162,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 93%] Linking CXX executable vcfdiff -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdiff.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o -o vcfdiff -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl -[ 94%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_multid_vector.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_multid_vector.cc.o -MF CMakeFiles/ctests.dir/src/test_multid_vector.cc.o.d -o CMakeFiles/ctests.dir/src/test_multid_vector.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_multid_vector.cc -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 94%] Built target vcfdiff -[ 94%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_pb.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_pb.cc.o -MF CMakeFiles/ctests.dir/src/test_pb.cc.o.d -o CMakeFiles/ctests.dir/src/test_pb.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_pb.cc -[ 94%] Linking CXX executable test_sparse_array_api -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sparse_array_api.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o -o test_sparse_array_api ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx -/usr/bin/ld: CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o: in function `TempDir::create_temp_directory()': -./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -[ 94%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o -c /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_jni_init.cc -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 94%] Built target test_sparse_array_api -[ 94%] Building CXX object src/test/cpp/CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o -MF CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o.d -o CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc +[ 95%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o -MF CMakeFiles/ctests.dir/src/test_logger.cc.o.d -o CMakeFiles/ctests.dir/src/test_logger.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_logger.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, @@ -5110,22 +5178,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 94%] Linking CXX executable vcf_histogram -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf_histogram.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o -o vcf_histogram -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl -[ 95%] Linking CXX executable test_storage_buffer -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_storage_buffer.dir/link.txt --verbose=1 -[ 95%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o -o test_storage_buffer ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o -MF CMakeFiles/ctests.dir/src/test_logger.cc.o.d -o CMakeFiles/ctests.dir/src/test_logger.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_logger.cc -/usr/bin/ld: CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o: in function `TempDir::create_temp_directory()': -./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' [ 96%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o -MF CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o.d -o CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 96%] Built target test_storage_buffer -[ 96%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o -MF CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o.d -o CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_htslib_plugin.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, @@ -5140,63 +5194,52 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 96%] Linking CXX executable test_posixfs -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_posixfs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o -o test_posixfs ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx -In file included from /build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc:28: -/build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc: In member function 'virtual void OneQueryIntervalProcessor::process(const std::string&, const int64_t*, const genomic_interval_t&, const std::vector&)': -/build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc:296:37: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 296 | CHECK(genomic_fields.size() == m_attributes_size + 2); // Add '2' for REF and ALT fields - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -/build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc: In function 'void C_A_T_C_H_T_E_S_T_40()': -/build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc:589:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 589 | CHECK(num_threads == threads.size()); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/usr/bin/ld: CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o: in function `TempDir::create_temp_directory()': -./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' +[ 96%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o -MF CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o.d -o CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_htslib_plugin.cc +/build/genomicsdb-1.4.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc: In function 'void C_A_T_C_H_T_E_S_T_2()': +/build/genomicsdb-1.4.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc:390:59: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] + 390 | REQUIRE(bcf_hdr_nsamples(bag.hdr[GoldTestEnum::GOLD]) == query_config.get_num_rows_to_query()); [ 96%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o -MF CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o.d -o CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_alleles_combiner.cc -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 96%] Built target vcf_histogram [ 97%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o -MF CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o.d -o CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_gt_remapper.cc +[ 97%] Linking CXX executable vcf_histogram +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf_histogram.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o -o vcf_histogram -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl [ 97%] Linking CXX executable consolidate_genomicsdb_array cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/consolidate_genomicsdb_array.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o -o consolidate_genomicsdb_array -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl -[ 98%] Linking CXX executable vcf2genomicsdb -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2genomicsdb.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o -o vcf2genomicsdb -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 98%] Built target test_posixfs -[ 98%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_bgen.cc.o +[ 97%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_bgen.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_bgen.cc.o -MF CMakeFiles/ctests.dir/src/test_bgen.cc.o.d -o CMakeFiles/ctests.dir/src/test_bgen.cc.o -c /build/genomicsdb-1.4.4/src/test/cpp/src/test_bgen.cc -/build/genomicsdb-1.4.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc: In function 'void C_A_T_C_H_T_E_S_T_2()': -/build/genomicsdb-1.4.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc:390:59: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] - 390 | REQUIRE(bcf_hdr_nsamples(bag.hdr[GoldTestEnum::GOLD]) == query_config.get_num_rows_to_query()); +[ 98%] Linking CXX executable test_expressions +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_expressions.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o -o test_expressions ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 98%] Built target vcf2genomicsdb +[ 98%] Built target vcf_histogram +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 98%] Built target test_expressions make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 98%] Built target consolidate_genomicsdb_array -[ 98%] Linking CXX executable test_genomicsdb_importer +[ 99%] Linking CXX executable vcf2genomicsdb +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2genomicsdb.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o -o vcf2genomicsdb -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 99%] Built target vcf2genomicsdb +[ 99%] Linking CXX executable test_genomicsdb_importer cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_genomicsdb_importer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o -o test_genomicsdb_importer -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl -[ 99%] Linking CXX executable test_expressions -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_expressions.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o -o test_expressions ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -ldl -lmuparserx +[ 99%] Linking CXX executable vcf2genomicsdb_init +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2genomicsdb_init.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie CMakeFiles/vcf2genomicsdb_init.dir/src/vcf2genomicsdb_init.cc.o -o vcf2genomicsdb_init -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 99%] Built target vcf2genomicsdb_init make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 99%] Built target test_expressions +[ 99%] Built target test_genomicsdb_importer [100%] Linking CXX shared library libgenomicsdbjni.so cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/genomicsdbjni.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -shared -Wl,-soname,libgenomicsdbjni.so -o libgenomicsdbjni.so CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib libgenomicsdb.so.1.4.4 ../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl ../../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [100%] Built target genomicsdbjni -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[100%] Built target test_genomicsdb_importer -[100%] Linking CXX executable vcf2genomicsdb_init -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2genomicsdb_init.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie CMakeFiles/vcf2genomicsdb_init.dir/src/vcf2genomicsdb_init.cc.o -o vcf2genomicsdb_init -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[100%] Built target vcf2genomicsdb_init [100%] Linking CXX executable api_tests cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/api_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now CMakeFiles/api_tests.dir/src/ctest_main.cc.o CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o -o api_tests -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib ../../main/libgenomicsdb.a ../../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../../../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.9.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl @@ -5399,15 +5442,15 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 17.048 s -[INFO] Finished at: 2024-06-08T11:03:23-12:00 +[INFO] Total time: 39.619 s +[INFO] Finished at: 2023-05-08T07:03:05+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/genomicsdb-1.4.4' jh_build -O--buildsystem=cmake debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/genomicsdb-1.4.4' dh_auto_build - 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[2]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/genomicsdb-1.4.4 -B/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/CMakeFiles /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -5419,152 +5462,162 @@ make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/CMakeFiles/protobuf_ep.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-htslib /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-htslib /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/DependInfo.cmake --color= +Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". 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Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". 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Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". +[ 0%] Built target PROTOBUF_GENERATED_CXX_TARGET Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". +make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/depend Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/DependInfo.cmake --color= Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". -Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". -Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". -[ 0%] Built target protobuf_ep Consolidate compiler generated dependencies of target genomicsdb-hts -make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/resources /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build.make genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build +Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target TILEDB_CORE_OBJECTS -[ 13%] Built target genomicsdb-hts -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build.make genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build -[ 13%] Built target PROTOBUF_GENERATED_CXX_TARGET -make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". -[ 25%] Built target TILEDB_CORE_OBJECTS Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target TILEDB_CORE_OBJECTS Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build.make genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/depend -make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/depend Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +[ 13%] Built target genomicsdb-hts Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". -Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +[ 25%] Built target TILEDB_CORE_OBJECTS +make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/depend Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/DependInfo.cmake --color= Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". 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Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". @@ -5572,980 +5625,970 @@ Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +[ 25%] Built target tiledb_static Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +[ 26%] Built target tiledb_shared Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/depend Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". -Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". -Dependencies file 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"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build -make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 25%] Built target tiledb_static -make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/depend -[ 26%] Built target tiledb_shared make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/depend +Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/depend +Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". +Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu 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genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/DependInfo.cmake --color= -Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target test_array_schema +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/depend +make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target test_array_schema Consolidate compiler generated dependencies of target test_print_array_schema -make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/depend +make -f genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/depend +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/compiler_depend.internal". -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build -Consolidate compiler generated dependencies of target test_print_book_keeping -make -f genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/depend +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target test_array_iterator +Consolidate compiler generated dependencies of target test_print_book_keeping Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build -make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/depend -make -f genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/depend make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build +Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target test_sparse_array_benchmark +Consolidate compiler generated dependencies of target test_array_iterator +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/compiler_depend.internal". -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/DependInfo.cmake --color= +[ 27%] Built target test_array_schema make -f genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build -Consolidate compiler generated dependencies of target test_sparse_array_benchmark make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_array_schema_api -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target GenomicsDB_library_object_files +[ 28%] Built target test_print_array_schema Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target test_dense_array_api +make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build -make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build -Consolidate compiler generated dependencies of target test_dense_array_api -Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/compiler_depend.internal". +make -f genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target test_sparse_array_api -Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/compiler_depend.internal". +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target test_codec +Consolidate compiler generated dependencies of target GenomicsDB_library_object_files make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target test_tiledb_utils make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build -make -f genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build +[ 29%] Built target test_print_book_keeping +[ 30%] Built target test_sparse_array_benchmark +[ 31%] Built target test_array_iterator +[ 31%] Built target test_array_schema_api +make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/depend +[ 31%] Built target test_dense_array_api +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/depend +Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/compiler_depend.internal". +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/depend +Consolidate compiler generated dependencies of target test_sparse_array_api make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build'. +make[4]: Nothing to be done for 'src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/compiler_depend.internal". +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/DependInfo.cmake --color= +Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target test_tiledb_utils Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 27%] Built target test_array_schema make -f genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build +Consolidate compiler generated dependencies of target test_codec Consolidate compiler generated dependencies of target test_codec_filter -make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target test_expressions +make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 46%] Built target GenomicsDB_library_object_files +Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/compiler_depend.internal". +make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build +Consolidate compiler generated dependencies of target test_mem_utils make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 28%] Built target test_print_array_schema -[ 29%] Built target test_print_book_keeping -[ 30%] Built target test_array_iterator -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/depend -[ 30%] Built target test_sparse_array_api -[ 30%] Built target test_array_schema_api -[ 31%] Built target test_sparse_array_benchmark -[ 31%] Built target test_dense_array_api -make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 46%] Built target test_sparse_array_api make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/depend -make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/depend +[ 46%] Built target test_tiledb_utils +[ 47%] Built target test_codec_filter make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/DependInfo.cmake --color= -[ 32%] Built target test_codec -[ 32%] Built target test_tiledb_utils -[ 47%] Built target GenomicsDB_library_object_files -make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/depend -[ 48%] Built target test_codec_filter -make -f genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/depend +make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/depend +[ 48%] Built target test_codec +[ 49%] Built target test_expressions make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/depend -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/depend +make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/depend +[ 50%] Built target test_mem_utils make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/depend +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/depend -Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/depend +Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/src/misc/test_uri.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/depend -Consolidate compiler generated dependencies of target test_mem_utils -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/src/misc/test_uri.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/compiler_depend.internal". -Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/compiler_depend.internal". +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/depend Consolidate compiler generated dependencies of target test_uri -Consolidate compiler generated dependencies of target test_expressions -make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/compiler_depend.internal". -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/src/tiledb_array_aio_write_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_array_aio_write_dense -Consolidate compiler generated dependencies of target test_utils +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build +Consolidate compiler generated dependencies of target test_utils +make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build'. +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_posixfs -Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/compiler_depend.internal". -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/compiler_depend.internal". +make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_storage_buffer -make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build -Consolidate compiler generated dependencies of target tiledb_array_consolidate -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/src/tiledb_array_aio_read_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_array_aio_read_dense -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_array_iterator_dense make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/src/tiledb_array_create_sparse.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/src/tiledb_array_aio_read_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target tiledb_array_create_sparse -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/src/tiledb_array_aio_write_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build +Consolidate compiler generated dependencies of target tiledb_array_aio_read_dense +make -f genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target tiledb_array_consolidate +Consolidate compiler generated dependencies of target tiledb_array_aio_write_dense make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_create_dense make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 49%] Built target test_uri -[ 50%] Built target test_expressions -[ 51%] Built target test_mem_utils -[ 51%] Built target test_utils -[ 52%] Built target tiledb_array_aio_read_dense -[ 53%] Built target test_posixfs -[ 53%] Built target test_storage_buffer +[ 50%] Built target test_utils +[ 51%] Built target test_uri +[ 51%] Built target test_posixfs +[ 52%] Built target test_storage_buffer +[ 53%] Built target tiledb_array_aio_read_dense +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/depend +[ 54%] Built target tiledb_array_aio_write_dense +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/depend +[ 55%] Built target tiledb_array_create_dense +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/src/tiledb_array_create_sparse.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/depend -[ 54%] Built target tiledb_array_aio_write_dense -[ 54%] Built target tiledb_array_consolidate +Consolidate compiler generated dependencies of target tiledb_array_create_sparse +[ 55%] Built target tiledb_array_consolidate +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_array_iterator_dense make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/src/tiledb_array_iterator_sparse.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/compiler_depend.internal". +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build +Consolidate compiler generated dependencies of target tiledb_array_iterator_sparse +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/src/tiledb_array_iterator_sparse_filter.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_array_iterator_sparse_filter +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/compiler_depend.internal". +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build +Consolidate compiler generated dependencies of target tiledb_array_parallel_consolidate_dense +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 56%] Built target tiledb_array_create_sparse +[ 56%] Built target tiledb_array_iterator_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/depend -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/DependInfo.cmake --color= -[ 55%] Built target tiledb_array_create_sparse -[ 55%] Built target tiledb_array_iterator_dense +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/depend +[ 57%] Built target tiledb_array_iterator_sparse make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/depend -[ 56%] Built target tiledb_array_create_dense -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/depend +[ 57%] Built target tiledb_array_parallel_consolidate_dense +[ 58%] Built target tiledb_array_iterator_sparse_filter +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/DependInfo.cmake --color= -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/src/tiledb_array_iterator_sparse.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/depend -Consolidate compiler generated dependencies of target tiledb_array_iterator_sparse -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/depend +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/depend +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/DependInfo.cmake --color= +Consolidate compiler generated dependencies of target tiledb_array_parallel_read_dense_1 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/depend +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/src/tiledb_array_iterator_sparse_filter.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/compiler_depend.internal". -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_array_iterator_sparse_filter +Consolidate compiler generated dependencies of target tiledb_array_parallel_read_dense_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build Consolidate compiler generated dependencies of target tiledb_array_parallel_consolidate_sparse -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_array_parallel_consolidate_dense -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_array_parallel_read_dense_1 -Consolidate compiler generated dependencies of target tiledb_array_parallel_read_dense_2 -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target tiledb_array_parallel_read_sparse_2 -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/compiler_depend.internal". -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build +Consolidate compiler generated dependencies of target tiledb_array_parallel_read_sparse_2 Consolidate compiler generated dependencies of target tiledb_array_parallel_read_mpi_io_dense Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build'. +Consolidate compiler generated dependencies of target tiledb_array_parallel_read_sparse_1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target tiledb_array_parallel_write_dense_1 -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/compiler_depend.internal". -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_array_parallel_write_dense_2 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target tiledb_array_parallel_read_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 57%] Built target tiledb_array_iterator_sparse +Consolidate compiler generated dependencies of target tiledb_array_parallel_write_dense_1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build +[ 59%] Built target tiledb_array_parallel_read_dense_1 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 59%] Built target tiledb_array_parallel_read_dense_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/depend +[ 59%] Built target tiledb_array_parallel_read_sparse_1 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 59%] Built target tiledb_array_iterator_sparse_filter -[ 59%] Built target tiledb_array_parallel_consolidate_sparse -[ 60%] Built target tiledb_array_parallel_read_dense_1 -[ 61%] Built target tiledb_array_parallel_read_mpi_io_dense -[ 61%] Built target tiledb_array_parallel_consolidate_dense -[ 61%] Built target tiledb_array_parallel_read_dense_2 +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/DependInfo.cmake --color= +[ 60%] Built target tiledb_array_parallel_read_mpi_io_dense +[ 61%] Built target tiledb_array_parallel_consolidate_sparse make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/depend [ 62%] Built target tiledb_array_parallel_read_sparse_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/depend +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/depend +[ 63%] Built target tiledb_array_parallel_write_dense_1 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/DependInfo.cmake --color= -[ 62%] Built target tiledb_array_parallel_write_dense_2 -[ 62%] Built target tiledb_array_parallel_read_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/depend -[ 63%] Built target tiledb_array_parallel_write_dense_1 +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_array_parallel_write_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/depend -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/depend -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/depend +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_array_parallel_write_sparse_1 +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/DependInfo.cmake --color= Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_parallel_write_sparse_2 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/depend +Consolidate compiler generated dependencies of target tiledb_array_parallel_write_sparse_1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/DependInfo.cmake --color= +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_primitive +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/compiler_depend.internal". -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build Consolidate compiler generated dependencies of target tiledb_array_read_dense_1 -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/compiler_depend.internal". -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target tiledb_array_read_dense_sorted make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_array_read_dense_2 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_read_dense_3 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target tiledb_array_read_sparse_1 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/compiler_depend.internal". +[ 63%] Built target tiledb_array_parallel_write_dense_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target tiledb_array_read_dense_2 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 64%] Built target tiledb_array_parallel_write_sparse_2 +[ 65%] Built target tiledb_array_parallel_write_sparse_1 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/depend +[ 66%] Built target tiledb_array_read_dense_1 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build'. +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/DependInfo.cmake --color= +[ 67%] Built target tiledb_array_read_dense_2 +[ 67%] Built target tiledb_array_primitive +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/depend +[ 67%] Built target tiledb_array_read_dense_3 +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/depend +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/DependInfo.cmake --color= +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_array_read_dense_sorted +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/depend +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/compiler_depend.internal". +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build Consolidate compiler generated dependencies of target tiledb_array_read_sparse_2 +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target tiledb_array_read_sparse_1 +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/depend Consolidate compiler generated dependencies of target tiledb_array_read_sparse_filter_1 -[ 64%] Built target tiledb_array_parallel_write_sparse_1 -[ 64%] Built target tiledb_array_primitive +Consolidate compiler generated dependencies of target tiledb_array_read_sparse_filter_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build'. +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 65%] Built target tiledb_array_read_dense_1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 66%] Built target tiledb_array_parallel_write_sparse_2 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/compiler_depend.internal". +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build +Consolidate compiler generated dependencies of target tiledb_array_read_sparse_sorted +[ 68%] Built target tiledb_array_read_dense_sorted +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build +[ 69%] Built target tiledb_array_read_sparse_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 66%] Built target tiledb_array_read_dense_3 -[ 67%] Built target tiledb_array_read_dense_sorted -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/depend +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/depend -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/depend -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/depend +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/depend -[ 67%] Built target tiledb_array_read_sparse_1 -[ 68%] Built target tiledb_array_read_dense_2 +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target tiledb_array_update_dense_1 +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target tiledb_array_update_dense_2 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/DependInfo.cmake --color= -[ 69%] Built target tiledb_array_read_sparse_2 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/depend +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 69%] Built target tiledb_array_read_sparse_1 +[ 70%] Built target tiledb_array_read_sparse_filter_1 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/depend +[ 70%] Built target tiledb_array_read_sparse_filter_2 +[ 71%] Built target tiledb_array_read_sparse_sorted make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/depend +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/DependInfo.cmake --color= -[ 70%] Built target tiledb_array_read_sparse_filter_1 -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/compiler_depend.internal". +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/depend +[ 72%] Built target tiledb_array_update_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/DependInfo.cmake --color= -Consolidate compiler generated dependencies of target tiledb_array_read_sparse_filter_2 -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/compiler_depend.internal". -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/compiler_depend.internal". -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_array_update_dense_2 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/DependInfo.cmake --color= -Consolidate compiler generated dependencies of target tiledb_array_update_sparse_1 -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_array_read_sparse_sorted -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/depend -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target tiledb_array_update_dense_1 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/depend +[ 72%] Built target tiledb_array_update_dense_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/depend -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/depend +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/depend +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/DependInfo.cmake --color= -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_array_update_sparse_1 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/depend +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_array_write_dense_1 +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_array_write_dense_2 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/depend make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target tiledb_array_update_sparse_2 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build -Consolidate compiler generated dependencies of target tiledb_array_write_dense_sorted -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build'. +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_array_update_sparse_2 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_array_write_sparse_3 -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/compiler_depend.internal". -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build -Consolidate compiler generated dependencies of target tiledb_array_write_sparse_1 -Consolidate compiler generated dependencies of target tiledb_array_write_dense_1 -Consolidate compiler generated dependencies of target tiledb_array_write_sparse_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_array_write_sparse_1 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target tiledb_array_write_sparse_2 +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build +Consolidate compiler generated dependencies of target tiledb_array_write_dense_sorted make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build -Consolidate compiler generated dependencies of target tiledb_array_write_dense_2 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build'. +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_array_write_sparse_3 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 73%] Built target tiledb_array_update_sparse_1 make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build -[ 71%] Built target tiledb_array_update_sparse_1 -[ 71%] Built target tiledb_array_read_sparse_filter_2 -[ 71%] Built target tiledb_array_update_dense_2 -[ 71%] Built target tiledb_array_write_dense_sorted -[ 72%] Built target tiledb_array_read_sparse_sorted -[ 73%] Built target tiledb_array_update_dense_1 -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 73%] Built target tiledb_array_write_dense_1 +[ 74%] Built target tiledb_array_update_sparse_2 +[ 75%] Built target tiledb_array_write_dense_2 +[ 76%] Built target tiledb_array_write_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/depend +[ 76%] Built target tiledb_array_write_dense_sorted make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/depend -[ 74%] Built target tiledb_array_update_sparse_2 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/depend -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/depend +[ 76%] Built target tiledb_array_write_sparse_3 +[ 77%] Built target tiledb_array_write_sparse_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/depend -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/depend +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/DependInfo.cmake --color= -[ 75%] Built target tiledb_array_write_sparse_1 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/depend +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/DependInfo.cmake --color= -[ 75%] Built target tiledb_array_write_dense_1 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/depend +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/depend +Consolidate compiler generated dependencies of target tiledb_catching_errors +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/DependInfo.cmake --color= -[ 76%] Built target tiledb_array_write_sparse_2 -[ 76%] Built target tiledb_array_write_sparse_3 -[ 77%] Built target tiledb_array_write_dense_2 +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/compiler_depend.internal". -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/depend -Consolidate compiler generated dependencies of target tiledb_array_write_sparse_4 -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/depend -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/depend +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/DependInfo.cmake --color= -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/depend Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_clear_delete_move -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_catching_errors +Consolidate compiler generated dependencies of target tiledb_array_write_sparse_4 +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/compiler_depend.internal". +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build Consolidate compiler generated dependencies of target tiledb_delete +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target tiledb_config make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_config -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build +[ 78%] Built target tiledb_catching_errors Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/compiler_depend.internal". -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/compiler_depend.internal". +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_ls -Consolidate compiler generated dependencies of target tiledb_metadata_iterator -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/compiler_depend.internal". -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_ls_workspaces -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target tiledb_metadata_primitive -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/compiler_depend.internal". -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_metadata_consolidate -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target tiledb_metadata_create -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 78%] Built target tiledb_array_write_sparse_4 -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/compiler_depend.internal". +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target tiledb_ls_workspaces +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build +[ 78%] Built target tiledb_clear_delete_move make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 79%] Built target tiledb_array_write_sparse_4 +[ 80%] Built target tiledb_delete +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build'. +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/depend +[ 81%] Built target tiledb_config +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/depend +[ 81%] Built target tiledb_ls +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/depend +[ 82%] Built target tiledb_ls_workspaces +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/depend +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_metadata_consolidate +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/depend +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target tiledb_metadata_create make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build'. +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/DependInfo.cmake --color= +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build +Consolidate compiler generated dependencies of target tiledb_metadata_iterator make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/compiler_depend.internal". +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target tiledb_metadata_read +Consolidate compiler generated dependencies of target tiledb_metadata_primitive +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 78%] Built target tiledb_clear_delete_move -[ 79%] Built target tiledb_config -[ 80%] Built target tiledb_catching_errors -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/depend -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/DependInfo.cmake --color= -[ 80%] Built target tiledb_ls -[ 81%] Built target tiledb_delete -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/depend -[ 82%] Built target tiledb_ls_workspaces -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/depend +Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/compiler_depend.internal". +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target tiledb_metadata_update +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/DependInfo.cmake --color= -make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/depend +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 83%] Built target tiledb_metadata_consolidate +[ 83%] Built target tiledb_metadata_create +[ 84%] Built target tiledb_metadata_iterator +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/depend +[ 84%] Built target tiledb_metadata_primitive make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/DependInfo.cmake --color= -[ 83%] Built target tiledb_metadata_consolidate +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/DependInfo.cmake --color= -make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/depend +[ 85%] Built target tiledb_metadata_read +make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/tiledbgenomicsdb.dir/DependInfo.cmake --color= -[ 83%] Built target tiledb_metadata_create -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/compiler_depend.internal". +make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdb.dir/DependInfo.cmake --color= -Consolidate compiler generated dependencies of target tiledb_metadata_read -[ 84%] Built target tiledb_metadata_iterator -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build -[ 84%] Built target tiledb_metadata_primitive -Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_metadata_update -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 86%] Built target tiledb_metadata_update Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/compiler_depend.internal". -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_metadata_write -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target tiledb_workspace_group_create make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'src/main/CMakeFiles/tiledbgenomicsdb.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build +Consolidate compiler generated dependencies of target tiledb_workspace_group_create make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/build +make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'src/main/CMakeFiles/genomicsdb.dir/build'. +make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build -[ 85%] Built target tiledb_metadata_read +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build'. +make[4]: Nothing to be done for 'src/main/CMakeFiles/genomicsdb.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 86%] Built target tiledb_metadata_update -[ 87%] Built target genomicsdb -[ 87%] Built target tiledb_metadata_write -[ 87%] Built target tiledbgenomicsdb -[ 88%] Built target tiledb_workspace_group_create +[ 86%] Built target tiledbgenomicsdb make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/depend -make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/depend -make -f src/test/cpp/CMakeFiles/api_tests.dir/build.make src/test/cpp/CMakeFiles/api_tests.dir/depend -make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/depend -make -f tools/CMakeFiles/gt_mpi_gather.dir/build.make tools/CMakeFiles/gt_mpi_gather.dir/depend +[ 86%] Built target tiledb_metadata_write make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/DependInfo.cmake --color= -make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/depend +[ 87%] Built target tiledb_workspace_group_create +[ 88%] Built target genomicsdb +make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/DependInfo.cmake --color= +make -f src/test/cpp/CMakeFiles/api_tests.dir/build.make src/test/cpp/CMakeFiles/api_tests.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/DependInfo.cmake --color= -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/DependInfo.cmake --color= +make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/depend +Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". +Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". +Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". +Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". +Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/create_genomicsdb_workspace.dir/DependInfo.cmake --color= +make -f tools/CMakeFiles/gt_mpi_gather.dir/build.make tools/CMakeFiles/gt_mpi_gather.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/gt_mpi_gather.dir/DependInfo.cmake --color= +make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/depend +Consolidate compiler generated dependencies of target genomicsdbjni +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb_init.dir/DependInfo.cmake --color= -make -f tools/CMakeFiles/vcf2genomicsdb.dir/build.make tools/CMakeFiles/vcf2genomicsdb.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/DependInfo.cmake --color= -make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/depend -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/DependInfo.cmake --color= -make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/depend -Dependencies file "tools/CMakeFiles/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/create_genomicsdb_workspace.dir/compiler_depend.internal". -Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". -Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". -Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". -Dependencies file "tools/CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/compiler_depend.internal". -Dependencies file "tools/CMakeFiles/vcf2genomicsdb_init.dir/src/vcf2genomicsdb_init.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb_init.dir/compiler_depend.internal". +make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/build Dependencies file "src/test/cpp/CMakeFiles/api_tests.dir/src/ctest_main.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/compiler_depend.internal". -Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target create_genomicsdb_workspace -Dependencies file "src/test/cpp/CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/compiler_depend.internal". -Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/ctest_main.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". +make -f tools/CMakeFiles/vcf2genomicsdb.dir/build.make tools/CMakeFiles/vcf2genomicsdb.dir/depend Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_bgen.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_config.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target vcf2genomicsdb -Consolidate compiler generated dependencies of target vcf2genomicsdb_init +Dependencies file "src/test/cpp/CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target api_tests +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/DependInfo.cmake --color= +make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/depend Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". 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'/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_pb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". -make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/build +make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/depend +Dependencies file "tools/CMakeFiles/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/create_genomicsdb_workspace.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf_histogram.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'tools/CMakeFiles/create_genomicsdb_workspace.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target genomicsdbjni -Dependencies file "tools/CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/compiler_depend.internal". -Dependencies file 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'/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/build +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target ctests +Dependencies file "tools/CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'tools/CMakeFiles/vcf2genomicsdb.dir/build'. +make[4]: Nothing to be done for 'tools/CMakeFiles/create_genomicsdb_workspace.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/build +Dependencies file "tools/CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/compiler_depend.internal". make -f tools/CMakeFiles/gt_mpi_gather.dir/build.make tools/CMakeFiles/gt_mpi_gather.dir/build -make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/depend -Consolidate compiler generated dependencies of target ctests +Consolidate compiler generated dependencies of target vcfdiff +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/build +Consolidate compiler generated dependencies of target vcf2genomicsdb +Dependencies file "tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf_histogram.dir/compiler_depend.internal". +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target vcf_histogram make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'src/main/CMakeFiles/genomicsdbjni.dir/build'. +make[4]: Nothing to be done for 'tools/CMakeFiles/gt_mpi_gather.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 90%] Built target genomicsdbjni make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'tools/CMakeFiles/vcfdiff.dir/build'. +make[4]: Nothing to be done for 'src/test/cpp/CMakeFiles/ctests.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f tools/CMakeFiles/vcf2genomicsdb.dir/build.make tools/CMakeFiles/vcf2genomicsdb.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'tools/CMakeFiles/gt_mpi_gather.dir/build'. +make[4]: Nothing to be done for 'tools/CMakeFiles/vcf2genomicsdb_init.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/build +make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/DependInfo.cmake --color= -Dependencies file "tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf_histogram.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target vcf_histogram -[ 89%] Built target vcf2genomicsdb -[ 90%] Built target create_genomicsdb_workspace +make[4]: Nothing to be done for 'tools/CMakeFiles/vcf2genomicsdb.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 91%] Built target api_tests -[ 91%] Built target vcf2genomicsdb_init +make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'src/test/cpp/CMakeFiles/ctests.dir/build'. +make[4]: Nothing to be done for 'tools/CMakeFiles/vcfdiff.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/build +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make[4]: Nothing to be done for 'tools/CMakeFiles/vcf_histogram.dir/build'. +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +[ 91%] Built target create_genomicsdb_workspace +[ 92%] Built target api_tests +[ 92%] Built target gt_mpi_gather +[ 95%] Built target ctests +[ 95%] Built target vcf2genomicsdb_init +make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/depend +[ 96%] Built target vcf2genomicsdb +make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/DependInfo.cmake --color= make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/depend -make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/DependInfo.cmake --color= -Dependencies file "tools/CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/compiler_depend.internal". +make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/depend +[ 97%] Built target vcfdiff +[ 98%] Built target vcf_histogram make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make[4]: Nothing to be done for 'tools/CMakeFiles/vcf_histogram.dir/build'. -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 93%] Built target genomicsdbjni +Dependencies file "tools/CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target consolidate_genomicsdb_array make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/build -[ 94%] Built target vcfdiff -[ 94%] Built target gt_mpi_gather -[ 97%] Built target ctests Dependencies file "example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target test_genomicsdb_bcf_generator +Dependencies file "example/CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/consolidate_genomicsdb_array.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -[ 98%] Built target vcf_histogram -Consolidate compiler generated dependencies of target test_genomicsdb_bcf_generator make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build -Dependencies file "example/CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target test_genomicsdb_importer +make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' +make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target test_genomicsdb_importer [ 99%] Built target consolidate_genomicsdb_array -make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' -make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'example/CMakeFiles/test_genomicsdb_importer.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' @@ -6736,15 +6779,15 @@ GenomicsDB: org.genomicsdb.importer.extensions.VidMapExtensions VCF header has 2 lines with the same field name test_field and header line type -- only the first line is considered by GenomicsDB GenomicsDB: org.genomicsdb.importer.extensions.VidMapExtensions VCF header has 2 lines with the same field name test_field and header line type -- only the first line is considered by GenomicsDB ERROR StatusLogger Reconfiguration failed: No configuration found for '5cb0d902' at 'null' in 'null' -GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.007094695000000001,Cpu time(s),0.0073165999999999995 -GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.0038157899999999995,Cpu time(s),0.003514774 -GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.0014351099999999999,Cpu time(s),0.00125382 -GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.001109227,Cpu time(s),0.0012154029999999999 -GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.001605238,Cpu time(s),0.001559155 -GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),7.26728E-4,Cpu time(s),6.64628E-4 -GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.00369613,Cpu time(s),7.99929E-4 -GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.003246754,Cpu time(s),0.001084873 -[INFO] Tests run: 44, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 16.958 s - in TestSuite +GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.022234489,Cpu time(s),0.007869442999999999 +GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.015472890999999999,Cpu time(s),0.004209475 +GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.001363761,Cpu time(s),0.00138309 +GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.001214896,Cpu time(s),0.0010651249999999999 +GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.011077613,Cpu time(s),0.0029441349999999996 +GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6.25071E-4,Cpu time(s),7.25301E-4 +GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6.43591E-4,Cpu time(s),5.17754E-4 +GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.013192113,Cpu time(s),0.001362287 +[INFO] Tests run: 44, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 51.192 s - in TestSuite [INFO] [INFO] Results: [INFO] @@ -6753,15 +6796,15 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 33.728 s -[INFO] Finished at: 2024-06-08T11:04:02-12:00 +[INFO] Total time: 01:32 min +[INFO] Finished at: 2023-05-08T07:04:54+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/genomicsdb-1.4.4' dh_auto_test -O--buildsystem=cmake -Nlibgenomicsdb-java - cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 + cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=--verbose ARGS\+=-j15 make[1]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j16 +/usr/bin/ctest --force-new-ctest-process --verbose -j15 UpdateCTestConfiguration from :/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu @@ -6861,12 +6904,6 @@ 15: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_utils 15: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test 15: Test timeout computed to be: 10000000 -test 16 - Start 16: test_posixfs - -16: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_posixfs -16: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test -16: Test timeout computed to be: 10000000 1: [TileDB::ArraySchema] Error: Cannot set attributes; No attributes given. 1: [TileDB::ArraySchema] Error: Cannot set attributes; The number of attributes must be positive. 1: [TileDB::ArraySchema] Error: Cannot set attributes; Duplicate attribute names. @@ -7037,15 +7074,18 @@ 4: test cases: 1 | 1 passed 4: assertions: - none - 4: +5: =============================================================================== +5: All tests passed (527 assertions in 6 test cases) +5: 6: =============================================================================== 6: All tests passed (335 assertions in 13 test cases) 6: -9: [TileDB::utils] Error: (set_working_dir) Failed to set_working_dir as /tmp/TileDBTestI4por5/WORKSPACE.non-existent does not exist -9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTestUH7JbV/WORKSPACE errno=2(No such file or directory) -9: [TileDB::FileSystem] Error: (get_files) Cannot open directory path=/tmp/TileDBTestUH7JbV/WORKSPACE errno=2(No such file or directory) -9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTestrdlZPt/WORKSPACE errno=2(No such file or directory) -9: 7e820c3ee657b1a27a56a7be9d202a7a7e820c3ee657b1a27a56a7be9d202a7a[TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTesteUkAW6/test_file -9: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTesteUkAW6/test_file +9: [TileDB::utils] Error: (set_working_dir) Failed to set_working_dir as /tmp/TileDBTestl9esv0/WORKSPACE.non-existent does not exist +9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTestGJdmUa/WORKSPACE errno=2(No such file or directory) +9: [TileDB::FileSystem] Error: (get_files) Cannot open directory path=/tmp/TileDBTestGJdmUa/WORKSPACE errno=2(No such file or directory) +9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTestQDXClN/WORKSPACE errno=2(No such file or directory) +9: 7e820c3ee657b1a27a56a7be9d202a7a7e820c3ee657b1a27a56a7be9d202a7a[TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTest1Es64O/test_file +9: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTest1Es64O/test_file 10: [TileDB::utils] Error: (gzip_handle_error) Cannot decompress with GZIP: inflate error: Z_BUF_ERROR 10: [TileDB::Codec] Error: Could not decompress with GZIP. 10: [TileDB::utils] Error: (gzip_handle_error) Cannot decompress with GZIP: inflate error: Z_BUF_ERROR @@ -7087,48 +7127,98 @@ 11: =============================================================================== 11: All tests passed (192 assertions in 2 test cases) 11: -13: Sat Jun 8 11:04:02 2024 Memory stats Tracking memory usage START size=6MB resident=3MB share=3MB text=404KB lib=0 data=528KB dt=0 +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +13: Mon May 8 07:04:56 2023 Memory stats Tracking memory usage START size=6MB resident=3MB share=3MB text=404KB lib=0 data=528KB dt=0 14: =============================================================================== 14: All tests passed (58 assertions in 1 test case) 14: - 1/21 Test #1: test_array_schema ................ Passed 0.05 sec + 1/21 Test #1: test_array_schema ................ Passed 0.27 sec +test 16 + Start 16: test_posixfs + +16: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_posixfs +16: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test +16: Test timeout computed to be: 10000000 + 2/21 Test #2: test_print_array_schema .......... Passed 0.27 sec test 17 Start 17: test_storage_buffer 17: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_storage_buffer 17: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test 17: Test timeout computed to be: 10000000 - 2/21 Test #2: test_print_array_schema .......... Passed 0.06 sec + 3/21 Test #3: test_print_book_keeping .......... Passed 0.27 sec test 18 Start 18: ci_tests 18: Test command: /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/run_examples.sh 18: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples 18: Test timeout computed to be: 10000000 - 3/21 Test #3: test_print_book_keeping .......... Passed 0.07 sec + 4/21 Test #4: test_sparse_array_benchmark ...... Passed 0.26 sec test 19 Start 19: ctests 19: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests "-d" "yes" 19: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp 19: Test timeout computed to be: 10000000 - 4/21 Test #4: test_sparse_array_benchmark ...... Passed 0.08 sec + 5/21 Test #5: test_array_iterator .............. Passed 0.26 sec test 20 Start 20: api_tests 20: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/api_tests "-d" "yes" 20: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp 20: Test timeout computed to be: 10000000 - 5/21 Test #6: test_array_schema_api ............ Passed 0.09 sec + 6/21 Test #6: test_array_schema_api ............ Passed 0.27 sec test 21 Start 21: tools_tests 21: Test command: /build/genomicsdb-1.4.4/tests/test_tools.sh "/build/genomicsdb-1.4.4/tests/inputs/vcfs" "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools" 21: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools 21: Test timeout computed to be: 10000000 - 6/21 Test #10: test_codec ....................... Passed 0.10 sec - 7/21 Test #11: test_codec_filter ................ Passed 0.09 sec - 8/21 Test #14: test_uri ......................... Passed 0.08 sec + 7/21 Test #10: test_codec ....................... Passed 0.22 sec + 8/21 Test #11: test_codec_filter ................ Passed 0.21 sec + 9/21 Test #14: test_uri ......................... Passed 0.16 sec +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Index to variable "a1" is out of bounds. +12: [TileDB::Expression] Error: (Expression) Attribute a2 in expression filter not present in the array schema +12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: +12: Undefined token "a2" found at position 0. 15: [TileDB::utils] Error: (RLE_compress) Failed compressing with RLE; invalid input buffer format 15: [TileDB::utils] Error: (RLE_compress) Failed compressing with RLE; output buffer overflow 15: [TileDB::utils] Error: (RLE_compress_coords_row) Failed compressing coordinates with RLE; invalid buffer format @@ -7145,77 +7235,32 @@ 15: =============================================================================== 15: All tests passed (86 assertions in 6 test cases) 15: - 9/21 Test #15: test_utils ....................... Passed 0.08 sec -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Index to variable "a1" is out of bounds. -12: [TileDB::Expression] Error: (Expression) Attribute a2 in expression filter not present in the array schema -12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: -12: Undefined token "a2" found at position 0. -12: [TileDB::Expression] Error: (Expression) Expression parsing for dense arrays not yet implemented -12: =============================================================================== -12: All tests passed (3009 assertions in 80 test cases) -12: -10/21 Test #12: test_expressions ................. Passed 0.09 sec -16: [TileDB::FileSystem] Error: (create_dir) Cannot create directory; Directory already exists path=/tmp/TileDBTest7WYup9/test_posixfs_dirdir +10/21 Test #15: test_utils ....................... Passed 0.14 sec +16: [TileDB::FileSystem] Error: (create_dir) Cannot create directory; Directory already exists path=/tmp/TileDBTestBMdo04/test_posixfs_dirdir 16: [TileDB::FileSystem] Error: (create_dir) Cannot create directory path=/non-existent-dir/foo errno=2(No such file or directory) -16: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/tmp/TileDBTest7WYup9/test_posixfs_dirdir errno=21(Is a directory) -16: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/tmp/TileDBTest7WYup9/test_posixfs_dirdir errno=21(Is a directory) +16: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/tmp/TileDBTestBMdo04/test_posixfs_dirdir errno=21(Is a directory) +16: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/tmp/TileDBTestBMdo04/test_posixfs_dirdir errno=21(Is a directory) 16: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=non-existent-dir errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (move_path) Cannot rename path path=non-existent-dir errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (delete_dir) Could not recursively delete directory path=non-existent-dir errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (get_files) Cannot open directory path=non-existent-dir errno=2(No such file or directory) -16: [TileDB::FileSystem] Error: (delete_file) Cannot remove file path=/tmp/TileDBTestNeWuNj/test_posixfs_dirfile/foo1 errno=2(No such file or directory) -16: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestD2i8HJ/test_posixfs_dirread_write/foo -16: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestD2i8HJ/test_posixfs_dirread_write/foo -16: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestD2i8HJ/test_posixfs_dirread_write/foo +16: [TileDB::FileSystem] Error: (delete_file) Cannot remove file path=/tmp/TileDBTestqiPgQ8/test_posixfs_dirfile/foo1 errno=2(No such file or directory) +16: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestinE5vy/test_posixfs_dirread_write/foo +16: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestinE5vy/test_posixfs_dirread_write/foo +16: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestinE5vy/test_posixfs_dirread_write/foo 16: [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-dir/foo errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=non-existent-dir/foo errno=2(No such file or directory) -5: =============================================================================== -5: All tests passed (527 assertions in 6 test cases) -5: -11/21 Test #5: test_array_iterator .............. Passed 0.11 sec -17: [TileDB::StorageBuffer] Error: (StorageBuffer) Cannot perform buffered reads or writes as there is no buffer chunk size set path=/tmp/TileDBTestqe7sPx/test-file -17: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/tmp/TileDBTestqe7sPx/test-file-non-existent errno=2(No such file or directory) -17: [TileDB::StorageBuffer] Error: (StorageBuffer) Cannot perform buffered reads or writes as there is no buffer chunk size set path=/tmp/TileDBTestqe7sPx/test-file -17: [TileDB::StorageBuffer] Error: (read_buffer) Cannot read past the filesize from buffer path=/tmp/TileDBTestqe7sPx/test-file +16: [TileDB::FileSystem] Error: (read_from_file) Cannot open simultaneously for reads/writes path=test_posixfs_dir_locking/foo +16: [TileDB::FileSystem] Error: (~PosixFS) File does not seem to be closed path=test_dir_locking1/foo_sync +16: [TileDB::FileSystem] Error: (~PosixFS) File does not seem to be closed path=test_dir_locking1/foo_no_close +16: =============================================================================== +16: All tests passed (258 assertions in 11 test cases) +16: +11/21 Test #16: test_posixfs ..................... Passed 0.13 sec +17: [TileDB::StorageBuffer] Error: (StorageBuffer) Cannot perform buffered reads or writes as there is no buffer chunk size set path=/tmp/TileDBTestLuoCaC/test-file +17: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/tmp/TileDBTestLuoCaC/test-file-non-existent errno=2(No such file or directory) +17: [TileDB::StorageBuffer] Error: (StorageBuffer) Cannot perform buffered reads or writes as there is no buffer chunk size set path=/tmp/TileDBTestLuoCaC/test-file +17: [TileDB::StorageBuffer] Error: (read_buffer) Cannot read past the filesize from buffer path=/tmp/TileDBTestLuoCaC/test-file 17: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/non-existent-file errno=13(Permission denied) 17: [TileDB::StorageBuffer] Error: (write_buffer) Cannot write bytes path=/non-existent-file errno=13(Permission denied) 17: [TileDB::StorageBuffer] Error: (finalize) Could not finalize buffer after compression path=/non-existent-file errno=13(Permission denied) @@ -7230,22 +7275,23 @@ 17: [TileDB::StorageBuffer] Error: (write_buffer) Compression type=1000 not supported in StorageBuffer 17: [TileDB::StorageBuffer] Error: (finalize) Could not finalize buffer after compression path=/non-existent-file errno=2(No such file or directory) 17: [TileDB::StorageBuffer] Error: (read_buffer) Compression type=1000 for read_buffer not supported for CompressedStorageBuffer -17: [TileDB::StorageBuffer] Error: (read_buffer) Cannot read past the filesize from buffer path=/tmp/TileDBTestPEC9tb/compressed_foo +17: [TileDB::StorageBuffer] Error: (read_buffer) Cannot read past the filesize from buffer path=/tmp/TileDBTests7F4l5/compressed_foo 18: Example 1: Running ./tiledb_workspace_group_create... -16: [TileDB::FileSystem] Error: (read_from_file) Cannot open simultaneously for reads/writes path=test_posixfs_dir_locking/foo -16: [TileDB::FileSystem] Error: (~PosixFS) File does not seem to be closed path=test_dir_locking1/foo_sync -16: [TileDB::FileSystem] Error: (~PosixFS) File does not seem to be closed path=test_dir_locking1/foo_no_close -16: =============================================================================== -16: All tests passed (258 assertions in 11 test cases) -16: 18: Example 1: Done running ./tiledb_workspace_group_create -12/21 Test #16: test_posixfs ..................... Passed 0.08 sec 18: Example 2: Running ./tiledb_ls_workspaces... +12: [TileDB::Expression] Error: (Expression) Expression parsing for dense arrays not yet implemented +12: =============================================================================== +12: All tests passed (3009 assertions in 80 test cases) +12: +12/21 Test #12: test_expressions ................. Passed 0.24 sec 20: 0.000 s: api get_version 20: 0.000 s: api empty_args -19: 0.001 s: Check loader configuration with json file -19: 0.000 s: Check configuration with json file -19: 0.000 s: Check configuration with json file and shared posifs optim +18: my_workspace +18: Example 2: Done running ./tiledb_ls_workspaces +18: Example 3: Running ./tiledb_array_create_dense... +19: 0.017 s: Check loader configuration with json file +19: 0.001 s: Check configuration with json file +19: 0.001 s: Check configuration with json file and shared posifs optim 19: 0.001 s: Compare configuration with json file and string 19: 0.000 s: genotype_ordering haploid_5_alleles 19: 0.000 s: genotype_ordering diploid_2_alleles @@ -7262,11 +7308,13 @@ 19: 0.000 s: multid_vector 2D_float_test 19: 0.000 s: multid_vector 2D_tuple_test 19: 0.000 s: pb_query_config_test -19: 0.003 s: pb_vid_mapping_test -19: 11:04:02.544 INFO NativeGenomicsDB - pid=3167179 tid=3167179 This is a test -19: 11:04:02.544 WARN NativeGenomicsDB - pid=3167179 tid=3167179 This is a test -19: 11:04:02.544 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 This is a test -19: 11:04:02.544 DEBUG NativeGenomicsDB - pid=3167179 tid=3167179 This is a test +18: Example 3: Done running ./tiledb_array_create_dense +18: Example 4: Running ./tiledb_array_create_sparse... +19: 0.019 s: pb_vid_mapping_test +19: 07:04:56.475 INFO NativeGenomicsDB - pid=2673112 tid=2673112 This is a test +19: 07:04:56.475 WARN NativeGenomicsDB - pid=2673112 tid=2673112 This is a test +19: 07:04:56.475 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 This is a test +19: 07:04:56.475 DEBUG NativeGenomicsDB - pid=2673112 tid=2673112 This is a test 19: This is a test 19: This is a test 19: This is a test @@ -7274,76 +7322,60 @@ 19: This is a once_only test 19: Trying format Hello1 Hello2 19: 0.000 s: test logger -19: 11:04:02.544 INFO NativeGenomicsDB - pid=3167179 tid=3167179 i=1 str=This is a test -19: 11:04:02.544 WARN NativeGenomicsDB - pid=3167179 tid=3167179 i=2 str=This is a test -19: 11:04:02.544 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 i=3 str=This is a test -19: 11:04:02.544 DEBUG NativeGenomicsDB - pid=3167179 tid=3167179 i=4 str=This is a test -19: 11:04:02.544 INFO NativeGenomicsDB - pid=3167179 tid=3167179 i=6 str=This is a once_only test -19: 11:04:02.544 WARN NativeGenomicsDB - pid=3167179 tid=3167179 i=7 str=This is a once_only test +19: 07:04:56.476 INFO NativeGenomicsDB - pid=2673112 tid=2673112 i=1 str=This is a test +19: 07:04:56.476 WARN NativeGenomicsDB - pid=2673112 tid=2673112 i=2 str=This is a test +19: 07:04:56.476 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 i=3 str=This is a test +19: 07:04:56.476 DEBUG NativeGenomicsDB - pid=2673112 tid=2673112 i=4 str=This is a test +19: 07:04:56.476 INFO NativeGenomicsDB - pid=2673112 tid=2673112 i=6 str=This is a once_only test +19: 07:04:56.476 WARN NativeGenomicsDB - pid=2673112 tid=2673112 i=7 str=This is a once_only test 19: 0.000 s: test logger format -19: 11:04:02.544 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 i=1 str=This is a test -19: 11:04:02.544 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 Test Exception -19: 11:04:02.544 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 Test Exception -19: 11:04:02.544 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 Test Exception -19: 11:04:02.544 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 Native Stack Trace: -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55e09625145e] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeb2e6) [0x55e0962452e6] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55e0961c6f2d] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55e0961dfd28] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55e0961e6923] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55e0961e8a0e] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55e0961e8f2a] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55e0961b9ce9] -19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7f226ecbd18a] -19: 11:04:02.544 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 Test Exception -19: 11:04:02.544 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 Native Stack Trace: -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55e09625145e] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeb2f6) [0x55e0962452f6] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55e0961c6f2d] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55e0961dfd28] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55e0961e6923] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55e0961e8a0e] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55e0961e8f2a] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55e0961b9ce9] -19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7f226ecbd18a] -19: 0.001 s: test logger exceptions -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55e09625145e] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeea6e) [0x55e096248a6e] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55e0961c6f2d] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55e0961dfd28] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55e0961e6923] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55e0961e8a0e] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55e0961e8f2a] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55e0961b9ce9] -19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7f226ecbd18a] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55e09625145e] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeea81) [0x55e096248a81] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55e0961c6f2d] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55e0961dfd28] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55e0961e6923] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55e0961e8a0e] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55e0961e8f2a] -19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55e0961b9ce9] -19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7f226ecbd18a] +19: 07:04:56.476 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 i=1 str=This is a test +19: 07:04:56.476 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Test Exception +19: 07:04:56.476 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Test Exception +19: 07:04:56.476 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Test Exception +19: 07:04:56.489 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Native Stack Trace: +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55f9e864545e] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeb2e6) [0x55f9e86392e6] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55f9e85baf2d] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55f9e85d3d28] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55f9e85da923] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55f9e85dca0e] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55f9e85dcf2a] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55f9e85adce9] +19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7fa98b58318a] +19: 07:04:56.490 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Test Exception +19: 07:04:56.490 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Native Stack Trace: +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55f9e864545e] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeb2f6) [0x55f9e86392f6] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55f9e85baf2d] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55f9e85d3d28] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55f9e85da923] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55f9e85dca0e] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55f9e85dcf2a] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55f9e85adce9] +19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7fa98b58318a] +19: 0.014 s: test logger exceptions +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55f9e864545e] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeea6e) [0x55f9e863ca6e] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55f9e85baf2d] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55f9e85d3d28] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55f9e85da923] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55f9e85dca0e] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55f9e85dcf2a] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55f9e85adce9] +19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7fa98b58318a] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55f9e864545e] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeea81) [0x55f9e863ca81] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55f9e85baf2d] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55f9e85d3d28] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55f9e85da923] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55f9e85dca0e] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55f9e85dcf2a] +19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55f9e85adce9] +19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7fa98b58318a] 19: This is a test 19: 0.000 s: test explicit logger -18: my_workspace -18: Example 2: Done running ./tiledb_ls_workspaces -18: Example 3: Running ./tiledb_array_create_dense... -18: Example 3: Done running ./tiledb_array_create_dense -19: 0.045 s: gvcf iterator -18: Example 4: Running ./tiledb_array_create_sparse... 18: Example 4: Done running ./tiledb_array_create_sparse -19: 0.028 s: columnar_gvcf_iterator_test -19: [TileDB] Error: No TileDB support for URL=dfdfd://ddd. -19: 11:04:02.619 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 htslib_plugin could not open file dfdfd://ddd No TileDB support for URL=dfdfd://ddd -19: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory) -19: 11:04:02.619 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 hts_plugin read /dfdfd/dfdfd/non-existent-file error [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory) -19: [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory) -19: 11:04:02.619 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 hts_plugin read non-existent-file error [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory) -19: 0.001 s: test htslib plugin -19: 0.000 s: alleles_combiner -19: 0.000 s: gt_remapper 18: Example 5: Running ./tiledb_array_primitive... 18: Array name: my_workspace/dense_arrays/my_array_A 18: Attributes: a1 a2 a3 @@ -7351,33 +7383,40 @@ 18: Array name: my_workspace/sparse_arrays/my_array_B 18: Attributes: a1 a2 a3 18: The array is sparse +19: 0.112 s: gvcf iterator 18: Example 5: Done running ./tiledb_array_primitive +20: 0.224 s: api query_variants direct DP 18: Example 6: Running ./tiledb_array_write_dense_1... +19: 0.087 s: columnar_gvcf_iterator_test +19: [TileDB] Error: No TileDB support for URL=dfdfd://ddd. +19: 07:04:56.690 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 htslib_plugin could not open file dfdfd://ddd No TileDB support for URL=dfdfd://ddd +19: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory) +19: 07:04:56.690 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 hts_plugin read /dfdfd/dfdfd/non-existent-file error [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory) +19: [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory) +19: 07:04:56.690 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 hts_plugin read non-existent-file error [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory) +19: 0.001 s: test htslib plugin +19: 0.000 s: alleles_combiner +19: 0.000 s: gt_remapper +20: 0.067 s: api query_variants direct DP with huge row range 18: Example 6: Done running ./tiledb_array_write_dense_1 18: Example 7: Running ./tiledb_array_write_sparse_1... +20: 0.069 s: api query_variants direct DP with huge disjoint row ranges 18: Example 7: Done running ./tiledb_array_write_sparse_1 -20: 0.163 s: api query_variants direct DP -20: 0.043 s: api query_variants direct DP with huge row range -20: 0.042 s: api query_variants direct DP with huge disjoint row ranges -20: 0.090 s: api query_variants direct DP with range composed of multiple points -20: 0.084 s: api query_variants direct DP with range composed of overlapping ranges -20: 0.015 s: api query_variants direct DP with invalid row range -20: 0.120 s: api query_variants direct DP and GT -9: =============================================================================== -9: All tests passed (10488234 assertions in 9 test cases) -9: -13/21 Test #9: test_tiledb_utils ................ Passed 0.81 sec -20: 0.145 s: api query_variants direct DP and GT with PP -20: 0.088 s: api query_variants with json -20: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/ws/t0_1_2/.__consolidation_lock -20: 0.087 s: api query variants with json string -13: Sat Jun 8 11:04:03 2024 Memory stats Tracking memory usage END size=6MB resident=3MB share=3MB text=404KB lib=0 data=528KB dt=0 +20: 0.120 s: api query_variants direct DP with range composed of multiple points +20: 0.139 s: api query_variants direct DP with range composed of overlapping ranges +20: 0.034 s: api query_variants direct DP with invalid row range +13: Mon May 8 07:04:57 2023 Memory stats Tracking memory usage END size=6MB resident=3MB share=3MB text=404KB lib=0 data=528KB dt=0 13: =============================================================================== 13: test cases: 1 | 1 passed 13: assertions: - none - 13: -14/21 Test #13: test_mem_utils ................... Passed 1.01 sec -20: 0.050 s: api query variants with enabled shared posixfs optimizations +13/21 Test #13: test_mem_utils ................... Passed 1.02 sec +20: 0.205 s: api query_variants direct DP and GT +20: 0.206 s: api query_variants direct DP and GT with PP +20: 0.153 s: api query_variants with json +20: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/ws/t0_1_2/.__consolidation_lock +20: 0.137 s: api query variants with json string +20: 0.067 s: api query variants with enabled shared posixfs optimizations 20: ---------------- 20: Interval:[0,1000000000] 20: @@ -7406,7 +7445,7 @@ 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] DP:76 -20: 0.145 s: api query_variant_calls direct +20: 0.222 s: api query_variant_calls direct 20: ---------------- 20: Interval:[0,1000000000] 20: @@ -7435,7 +7474,7 @@ 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 DP:76 -20: 0.130 s: api query_variant_calls direct DP and GT +20: 0.220 s: api query_variant_calls direct DP and GT 20: ---------------- 20: Interval:[0,1000000000] 20: @@ -7464,7 +7503,7 @@ 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 DP:76 -20: 0.135 s: api query_variant_calls direct DP and GT with PP +20: 0.219 s: api query_variant_calls direct DP and GT with PP 20: ---------------- 20: Interval:[0,1000000000] 20: @@ -7493,7 +7532,10 @@ 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] DP:76 -20: 0.059 s: api query_variant_calls with json +20: 0.107 s: api query_variant_calls with json +9: =============================================================================== +9: All tests passed (10488234 assertions in 9 test cases) +9: 20: ---------------- 20: Interval:[0,1000000000] 20: @@ -7522,6 +7564,7 @@ 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 DP:76 +14/21 Test #9: test_tiledb_utils ................ Passed 2.52 sec 20: ---------------- 20: Interval:[0,249250620] 20: @@ -7550,26 +7593,21 @@ 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 DP:76 -20: 0.057 s: api query_variant_calls with protobuf -20: 0.123 s: api generate_vcf direct -20: 0.041 s: api generate_vcf with json -20: 0.212 s: api generate_vcf with json multiple threads +20: 0.107 s: api query_variant_calls with protobuf +20: 0.220 s: api generate_vcf direct +20: 0.069 s: api generate_vcf with json +20: 1.988 s: api generate_vcf with json multiple threads 20: ---------------- 20: Interval:[0,1000000000] 20: 20: ---------------- 20: Interval:[0,1000000000] 20: -20: 0.054 s: api annotate query_variant_calls with test datasource 0 +20: 0.069 s: api annotate query_variant_calls with test datasource 0 20: =============================================================================== 20: All tests passed (731 assertions in 22 test cases) 20: -15/21 Test #20: api_tests ........................ Passed 1.94 sec -17: +++ we are here 2 -17: =============================================================================== -17: All tests passed (450703 assertions in 3 test cases) -17: -16/21 Test #17: test_storage_buffer .............. Passed 2.32 sec +15/21 Test #20: api_tests ........................ Passed 4.80 sec 18: Example 8: Running ./tiledb_ls... 18: my_workspace WORKSPACE 18: Example 8: Done running ./tiledb_ls @@ -7595,34 +7633,31 @@ 18: Example 9: Done running ./tiledb_array_read_dense_1 18: Example 10: Running ./tiledb_array_write_dense_2... 18: Example 10: Done running ./tiledb_array_write_dense_2 -19: 11:04:08.685 INFO NativeGenomicsDB - pid=3167179 tid=3167179 Plink progress 3452039 / 6904084 = 50.00% -19: 11:04:08.685 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 PL field for sample: HG00141 row: 0 column: 12277 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] -19: 11:04:08.685 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 GL field for sample: HG00141 row: 0 column: 12277 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] -19: 11:04:08.686 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 PL field for sample: HG00141 row: 0 column: 12299 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] -19: 11:04:08.686 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 GL field for sample: HG00141 row: 0 column: 12299 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] -19: 11:04:08.686 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 PL field for sample: HG01958 row: 1 column: 12299 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] -19: 11:04:08.686 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 GL field for sample: HG01958 row: 1 column: 12299 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] -19: 11:04:08.686 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 PL field for sample: HG00141 row: 0 column: 12399 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] -19: 11:04:08.686 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 GL field for sample: HG00141 row: 0 column: 12399 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] -19: 11:04:08.686 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 PL field for sample: HG01958 row: 1 column: 12399 contains a negative value or otherwise did not parse, full string: [0, 1, -2147483648] -19: 11:04:08.686 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 GL field for sample: HG01958 row: 1 column: 12399 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] -19: 11:04:08.686 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 GL field for sample: HG00141 row: 0 column: 12499 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan, nan, nan, nan] -19: 11:04:08.686 ERROR NativeGenomicsDB - pid=3167179 tid=3167179 PL field for sample: HG01958 row: 1 column: 12499 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648, -2147483648, -2147483648, -2147483648] -19: 11:04:08.686 WARN NativeGenomicsDB - pid=3167179 tid=3167179 GL probabilities at sample: HG01958 row: 1 column: 12499 sum to 0.8981071705534972, expected near 1. Generated BGEN may be invalid -19: 6.073 s: test bgen +19: 07:05:03.686 INFO NativeGenomicsDB - pid=2673112 tid=2673112 Plink progress 3452039 / 6904084 = 50.00% +19: 07:05:03.693 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 PL field for sample: HG00141 row: 0 column: 12277 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] +19: 07:05:03.693 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 GL field for sample: HG00141 row: 0 column: 12277 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] +19: 07:05:03.693 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 PL field for sample: HG00141 row: 0 column: 12299 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] +19: 07:05:03.693 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 GL field for sample: HG00141 row: 0 column: 12299 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] +19: 07:05:03.693 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 PL field for sample: HG01958 row: 1 column: 12299 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] +19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 GL field for sample: HG01958 row: 1 column: 12299 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] +19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 PL field for sample: HG00141 row: 0 column: 12399 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] +19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 GL field for sample: HG00141 row: 0 column: 12399 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] +19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 PL field for sample: HG01958 row: 1 column: 12399 contains a negative value or otherwise did not parse, full string: [0, 1, -2147483648] +19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 GL field for sample: HG01958 row: 1 column: 12399 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] +19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 GL field for sample: HG00141 row: 0 column: 12499 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan, nan, nan, nan] +19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 PL field for sample: HG01958 row: 1 column: 12499 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648, -2147483648, -2147483648, -2147483648] +19: 07:05:03.694 WARN NativeGenomicsDB - pid=2673112 tid=2673112 GL probabilities at sample: HG01958 row: 1 column: 12499 sum to 0.8981071705534972, expected near 1. Generated BGEN may be invalid +19: 7.050 s: test bgen 19: =============================================================================== 19: All tests passed (1425 assertions in 30 test cases) 19: -19: 11:04:08.693 DEBUG NativeGenomicsDB - pid=3167179 tid=3167179 Deleting htslib_fs_adapter tiledb_ctx_map -17/21 Test #19: ctests ........................... Passed 6.23 sec -7: 10% [=== ] 20% [====== ] 30% [========= ] 40% [============ ] 50% [=============== ] 60% [================== ] 70% [===================== ] 80% [======================= ] 89% [========================== ] 99% [============================= ] 10% [=== ] 20% [====== ] 30% [========= ] 40% [============ ] 50% [=============== ] 60% [================== ] 70% [===================== ] 80% [======================= ] 89% [========================== ] 99% [============================= ] =============================================================================== -7: All tests passed (135041850 assertions in 4 test cases) -7: -18/21 Test #7: test_dense_array_api ............. Passed 6.31 sec -8: 10% [=== ] 20% [====== ] 30% [========= ] 40% [============ ] 50% [=============== ] 60% [================== ] 70% [===================== ] 80% [======================= ] 89% [========================== ] 99% [============================= ] =============================================================================== -8: All tests passed (11396562 assertions in 14 test cases) -8: -19/21 Test #8: test_sparse_array_api ............ Passed 10.15 sec +19: 07:05:03.740 DEBUG NativeGenomicsDB - pid=2673112 tid=2673112 Deleting htslib_fs_adapter tiledb_ctx_map +16/21 Test #19: ctests ........................... Passed 7.60 sec +17: +++ we are here 2 +17: =============================================================================== +17: All tests passed (450703 assertions in 3 test cases) +17: +17/21 Test #17: test_storage_buffer .............. Passed 8.93 sec 18: Example 11: Running ./tiledb_array_read_dense_1... 18: a1 a2 (a3.first, a3.second) 18: ----------------------------------------- @@ -7679,6 +7714,10 @@ 18: Example 14: Done running ./tiledb_array_read_dense_1 18: Example 15: Running ./tiledb_array_update_dense_1... 18: Example 15: Done running ./tiledb_array_update_dense_1 +8: 10% [=== ] 20% [====== ] 30% [========= ] 40% [============ ] 50% [=============== ] 60% [================== ] 70% [===================== ] 80% [======================= ] 89% [========================== ] 99% [============================= ] =============================================================================== +8: All tests passed (15200383 assertions in 14 test cases) +8: +18/21 Test #8: test_sparse_array_api ............ Passed 20.67 sec 18: Example 16: Running ./tiledb_array_read_dense_1... 18: a1 a2 (a3.first, a3.second) 18: ----------------------------------------- @@ -7701,6 +7740,10 @@ 18: Example 16: Done running ./tiledb_array_read_dense_1 18: Example 17: Running ./tiledb_array_update_dense_2... 18: Example 17: Done running ./tiledb_array_update_dense_2 +7: 10% [=== ] 20% [====== ] 30% [========= ] 40% [============ ] 50% [=============== ] 60% [================== ] 70% [===================== ] 80% [======================= ] 89% [========================== ] 99% [============================= ] 10% [=== ] 20% [====== ] 30% [========= ] 40% [============ ] 50% [=============== ] 60% [================== ] 70% [===================== ] 80% [======================= ] 89% [========================== ] 99% [============================= ] =============================================================================== +7: All tests passed (109505881 assertions in 4 test cases) +7: +19/21 Test #7: test_dense_array_api ............. Passed 23.45 sec 18: Example 18: Running ./tiledb_array_read_dense_1... 18: a1 a2 (a3.first, a3.second) 18: ----------------------------------------- @@ -7912,12 +7955,12 @@ 18: 106 18: 107 18: Example 41: Done running ./tiledb_array_read_sparse_2 -20/21 Test #18: ci_tests ......................... Passed 47.24 sec -21/21 Test #21: tools_tests ...................... Passed 67.31 sec +20/21 Test #18: ci_tests ......................... Passed 50.63 sec +21/21 Test #21: tools_tests ...................... Passed 121.62 sec 100% tests passed, 0 tests failed out of 21 -Total Test time (real) = 67.41 sec +Total Test time (real) = 122.04 sec make[1]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake @@ -7952,15 +7995,15 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 1.949 s -[INFO] Finished at: 2024-06-08T11:05:19-12:00 +[INFO] Total time: 2.910 s +[INFO] Finished at: 2023-05-08T07:07:10+14:00 [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibgenomicsdb-java --base-directory=/build/genomicsdb-1.4.4 --non-explore Analysing pom.xml... mh_unpatchpoms -plibgenomicsdb-java make[1]: Leaving directory '/build/genomicsdb-1.4.4' dh_auto_install -O--buildsystem=cmake -Nlibgenomicsdb-java - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/genomicsdb-1.4.4/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/genomicsdb-1.4.4/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/genomicsdb-1.4.4 -B/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -8065,33 +8108,33 @@ dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' -dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' -dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' -dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' -dpkg-shlibdeps: warning: debian/libgenomicsdb0/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-hts.so contains an unresolvable reference to symbol deflateEnd: it's probably a plugin -dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' +dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' +dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' +dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' +dpkg-shlibdeps: warning: debian/libgenomicsdb0/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-hts.so contains an unresolvable reference to symbol lgamma: it's probably a plugin +dpkg-shlibdeps: warning: 14 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 libgenomicsdb-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: Depends field of package libgenomicsdb-dev: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: package libgenomicsdb-java: substitution variable ${maven:CompileDepends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'libgenomicsdb0' in '../libgenomicsdb0_1.4.4-3_amd64.deb'. +dpkg-deb: building package 'genomicsdb-tools-dbgsym' in '../genomicsdb-tools-dbgsym_1.4.4-3_amd64.deb'. +dpkg-deb: building package 'genomicsdb-tools' in '../genomicsdb-tools_1.4.4-3_amd64.deb'. dpkg-deb: building package 'libgenomicsdb-dev' in '../libgenomicsdb-dev_1.4.4-3_amd64.deb'. -dpkg-deb: building package 'libgenomicsdb-java' in '../libgenomicsdb-java_1.4.4-3_all.deb'. +dpkg-deb: building package 'libgenomicsdb0' in '../libgenomicsdb0_1.4.4-3_amd64.deb'. dpkg-deb: building package 'libgenomicsdb-jni' in '../libgenomicsdb-jni_1.4.4-3_amd64.deb'. +dpkg-deb: building package 'libgenomicsdb-java' in '../libgenomicsdb-java_1.4.4-3_all.deb'. dpkg-deb: building package 'libgenomicsdb-jni-dbgsym' in '../libgenomicsdb-jni-dbgsym_1.4.4-3_amd64.deb'. -dpkg-deb: building package 'genomicsdb-tools-dbgsym' in '../genomicsdb-tools-dbgsym_1.4.4-3_amd64.deb'. -dpkg-deb: building package 'genomicsdb-tools' in '../genomicsdb-tools_1.4.4-3_amd64.deb'. dpkg-deb: building package 'libgenomicsdb0-dbgsym' in '../libgenomicsdb0-dbgsym_1.4.4-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../genomicsdb_1.4.4-3_amd64.buildinfo dpkg-genchanges --build=binary -O../genomicsdb_1.4.4-3_amd64.changes @@ -8100,12 +8143,14 @@ 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/2304883/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2304883/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/2916162 and its subdirectories -I: Current time: Sat Jun 8 11:08:26 -12 2024 -I: pbuilder-time-stamp: 1717888106 +I: removing directory /srv/workspace/pbuilder/2304883 and its subdirectories +I: Current time: Mon May 8 07:13:31 +14 2023 +I: pbuilder-time-stamp: 1683479611