Diff of the two buildlogs: -- --- b1/build.log 2021-08-10 13:33:32.038668186 +0000 +++ b2/build.log 2021-08-10 13:38:21.971914556 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Aug 10 01:30:53 -12 2021 -I: pbuilder-time-stamp: 1628602253 +I: Current time: Tue Sep 13 09:56:34 +14 2022 +I: pbuilder-time-stamp: 1663012594 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Feb 5 19:27:30 2019 -12 +gpgv: Signature made Wed Feb 6 21:27:30 2019 +14 gpgv: using RSA key 3AFA757FAC6EA11D2FF45DF088D24287A2D898B1 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./blasr_5.3.2+dfsg-1.1.dsc @@ -28,136 +28,170 @@ dpkg-source: info: applying use_debian_packaged_pblibs.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/44749/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/47678/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/47678/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/47678/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=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(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=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='2f05dd66f2474272bd4e1e02260bb20a' - 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='44749' - PS1='# ' - PS2='> ' + INVOCATION_ID=59340c6d097f41e18bfd7dd4b711423e + 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=47678 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/tmp.pnP8gqpHvP/pbuilderrc_2g90 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.pnP8gqpHvP/b1 --logfile b1/build.log blasr_5.3.2+dfsg-1.1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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/tmp.pnP8gqpHvP/pbuilderrc_ovLQ --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.pnP8gqpHvP/b2 --logfile b2/build.log blasr_5.3.2+dfsg-1.1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-0.bpo.8-amd64 #1 SMP Debian 5.10.46-2~bpo10+1 (2021-07-22) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 6 20:25 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/44749/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 13 09:56 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 10 04:46 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/47678/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -319,7 +353,7 @@ Get: 102 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 meson all 0.49.2-1 [281 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] -Fetched 57.7 MB in 1s (65.0 MB/s) +Fetched 57.7 MB in 1s (50.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0: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 ... 19195 files and directories currently installed.) @@ -763,7 +797,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/blasr-5.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/blasr-5.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package blasr dpkg-buildpackage: info: source version 5.3.2+dfsg-1.1 dpkg-buildpackage: info: source distribution unstable @@ -815,18 +849,29 @@ make[1]: Entering directory '/build/blasr-5.3.2+dfsg' ln -s build obj-x86_64-linux-gnu dh_auto_build - cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j15 -v + cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j16 -v [1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h '' /build/blasr-5.3.2+dfsg @BLASR_GIT_SHA1@ '(.*)' /build/blasr-5.3.2+dfsg/git describe --always '--dirty=*' -[2/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -MF 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o.d' -o 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -c ../extrautils/SimpleShredder.cpp +[2/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -MF 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o.d' -o 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -c ../extrautils/ExciseRepeats.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, from /usr/include/pbseq/pbdata/FASTAReader.hpp:7, - from ../extrautils/SimpleShredder.cpp:6: + from ../extrautils/ExciseRepeats.cpp:3: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition -[3/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -MF 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o.d' -o 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -c ../extrautils/SuffixArrayToBWT.cpp +[3/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SALS.cpp.o' -MF 'blasr_impl@sta/extrautils_SALS.cpp.o.d' -o 'blasr_impl@sta/extrautils_SALS.cpp.o' -c ../extrautils/SALS.cpp +In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, + from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, + from /usr/include/pbseq/alignment/algorithms/sorting/MultikeyQuicksort.hpp:21, + from /usr/include/pbseq/alignment/algorithms/sorting/LightweightSuffixArray.hpp:8, + from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:13, + from ../extrautils/SALS.cpp:4: +/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined + #define USE_PBBAM + +: note: this is the location of the previous definition +[4/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -MF 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o.d' -o 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -c ../extrautils/SuffixArrayToBWT.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/bwt/Occ.hpp:8, from /usr/include/pbseq/alignment/bwt/BWT.hpp:7, @@ -867,53 +912,25 @@ /usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here case 4: //N ^~~~ -[4/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -MF 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o.d' -o 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -c ../extrautils/ExciseRepeats.cpp +[5/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -MF 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o.d' -o 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -c ../extrautils/BwtToSuffixArray.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, - from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, - from /usr/include/pbseq/pbdata/FASTAReader.hpp:7, - from ../extrautils/ExciseRepeats.cpp:3: -/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined - #define USE_PBBAM - -: note: this is the location of the previous definition -[5/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SALS.cpp.o' -MF 'blasr_impl@sta/extrautils_SALS.cpp.o.d' -o 'blasr_impl@sta/extrautils_SALS.cpp.o' -c ../extrautils/SALS.cpp -In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, - from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, - from /usr/include/pbseq/alignment/algorithms/sorting/MultikeyQuicksort.hpp:21, - from /usr/include/pbseq/alignment/algorithms/sorting/LightweightSuffixArray.hpp:8, - from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:13, - from ../extrautils/SALS.cpp:4: -/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined - #define USE_PBBAM - -: note: this is the location of the previous definition -[6/25] c++ -Isawriter@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'sawriter@exe/utils_SAWriter.cpp.o' -MF 'sawriter@exe/utils_SAWriter.cpp.o.d' -o 'sawriter@exe/utils_SAWriter.cpp.o' -c ../utils/SAWriter.cpp -In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, - from /usr/include/pbseq/alignment/algorithms/sorting/Karkkainen.hpp:4, - from ../utils/SAWriter.cpp:5: + from /usr/include/pbseq/alignment/bwt/Occ.hpp:8, + from /usr/include/pbseq/alignment/bwt/BWT.hpp:7, + from ../extrautils/BwtToSuffixArray.cpp:5: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition -[7/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_Evolve.cpp.o' -MF 'blasr_impl@sta/extrautils_Evolve.cpp.o.d' -o 'blasr_impl@sta/extrautils_Evolve.cpp.o' -c ../extrautils/Evolve.cpp +[6/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -MF 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o.d' -o 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -c ../extrautils/BuildSequenceDB.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, from /usr/include/pbseq/pbdata/FASTAReader.hpp:7, - from ../extrautils/Evolve.cpp:6: -/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined - #define USE_PBBAM - -: note: this is the location of the previous definition -[8/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -MF 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o.d' -o 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -c ../extrautils/BwtToSuffixArray.cpp -In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, - from /usr/include/pbseq/alignment/bwt/Occ.hpp:8, - from /usr/include/pbseq/alignment/bwt/BWT.hpp:7, - from ../extrautils/BwtToSuffixArray.cpp:5: + from ../extrautils/BuildSequenceDB.cpp:5: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition -[9/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -MF 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o.d' -o 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -c ../extrautils/PrintTupleCountTable.cpp +[7/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -MF 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o.d' -o 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -c ../extrautils/PrintTupleCountTable.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/tuples/DNATuple.hpp:15, from /usr/include/pbseq/alignment/tuples/CompressedDNATuple.hpp:4, @@ -922,27 +939,25 @@ #define USE_PBBAM : note: this is the location of the previous definition -[10/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SAModify.cpp.o' -MF 'blasr_impl@sta/extrautils_SAModify.cpp.o.d' -o 'blasr_impl@sta/extrautils_SAModify.cpp.o' -c ../extrautils/SAModify.cpp +[8/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_Evolve.cpp.o' -MF 'blasr_impl@sta/extrautils_Evolve.cpp.o.d' -o 'blasr_impl@sta/extrautils_Evolve.cpp.o' -c ../extrautils/Evolve.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, - from /usr/include/pbseq/alignment/algorithms/sorting/MultikeyQuicksort.hpp:21, - from /usr/include/pbseq/alignment/algorithms/sorting/LightweightSuffixArray.hpp:8, - from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:13, - from ../extrautils/SAModify.cpp:5: + from /usr/include/pbseq/pbdata/FASTAReader.hpp:7, + from ../extrautils/Evolve.cpp:6: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition -[11/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -MF 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o.d' -o 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -c ../extrautils/BuildSequenceDB.cpp +[9/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -MF 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o.d' -o 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -c ../extrautils/SimpleShredder.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, from /usr/include/pbseq/pbdata/FASTAReader.hpp:7, - from ../extrautils/BuildSequenceDB.cpp:5: + from ../extrautils/SimpleShredder.cpp:6: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition -[12/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -MF 'blasr_impl@sta/extrautils_SWMatcher.cpp.o.d' -o 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -c ../extrautils/SWMatcher.cpp +[10/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -MF 'blasr_impl@sta/extrautils_SWMatcher.cpp.o.d' -o 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -c ../extrautils/SWMatcher.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42, @@ -952,17 +967,15 @@ #define USE_PBBAM : note: this is the location of the previous definition -[13/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamToM4.cpp.o' -MF 'blasr_impl@sta/utils_SamToM4.cpp.o.d' -o 'blasr_impl@sta/utils_SamToM4.cpp.o' -c ../utils/SamToM4.cpp +[11/25] c++ -Isawriter@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'sawriter@exe/utils_SAWriter.cpp.o' -MF 'sawriter@exe/utils_SAWriter.cpp.o.d' -o 'sawriter@exe/utils_SAWriter.cpp.o' -c ../utils/SAWriter.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, - from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13, - from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42, - from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6, - from ../utils/SamToM4.cpp:21: + from /usr/include/pbseq/alignment/algorithms/sorting/Karkkainen.hpp:4, + from ../utils/SAWriter.cpp:5: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition -[14/25] c++ -ItoAfg@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'toAfg@exe/utils_ToAfg.cpp.o' -MF 'toAfg@exe/utils_ToAfg.cpp.o.d' -o 'toAfg@exe/utils_ToAfg.cpp.o' -c ../utils/ToAfg.cpp +[12/25] c++ -ItoAfg@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'toAfg@exe/utils_ToAfg.cpp.o' -MF 'toAfg@exe/utils_ToAfg.cpp.o.d' -o 'toAfg@exe/utils_ToAfg.cpp.o' -c ../utils/ToAfg.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:19, from /usr/include/pbseq/hdf/HDFArray.hpp:9, @@ -978,6 +991,27 @@ /usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (DataSetIException e) { ^ +[13/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SAModify.cpp.o' -MF 'blasr_impl@sta/extrautils_SAModify.cpp.o.d' -o 'blasr_impl@sta/extrautils_SAModify.cpp.o' -c ../extrautils/SAModify.cpp +In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, + from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, + from /usr/include/pbseq/alignment/algorithms/sorting/MultikeyQuicksort.hpp:21, + from /usr/include/pbseq/alignment/algorithms/sorting/LightweightSuffixArray.hpp:8, + from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:13, + from ../extrautils/SAModify.cpp:5: +/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined + #define USE_PBBAM + +: note: this is the location of the previous definition +[14/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamToM4.cpp.o' -MF 'blasr_impl@sta/utils_SamToM4.cpp.o.d' -o 'blasr_impl@sta/utils_SamToM4.cpp.o' -c ../utils/SamToM4.cpp +In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, + from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13, + from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42, + from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6, + from ../utils/SamToM4.cpp:21: +/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined + #define USE_PBBAM + +: note: this is the location of the previous definition [15/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' -MF 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o.d' -o 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' -c ../extrautils/StoreQualityByContextFromCmpH5.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:19, @@ -1008,17 +1042,7 @@ /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’ /usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] -[16/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -MF 'blasr_impl@sta/utils_SDPMatcher.cpp.o.d' -o 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -c ../utils/SDPMatcher.cpp -In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, - from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13, - from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42, - from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6, - from ../utils/SDPMatcher.cpp:8: -/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined - #define USE_PBBAM - -: note: this is the location of the previous definition -[17/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -MF 'blasr_impl@sta/utils_SamToCmpH5.cpp.o.d' -o 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -c ../utils/SamToCmpH5.cpp +[16/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -MF 'blasr_impl@sta/utils_SamToCmpH5.cpp.o.d' -o 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -c ../utils/SamToCmpH5.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:9, from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, @@ -1047,6 +1071,16 @@ /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’ /usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] +[17/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -MF 'blasr_impl@sta/utils_SDPMatcher.cpp.o.d' -o 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -c ../utils/SDPMatcher.cpp +In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, + from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13, + from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42, + from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6, + from ../utils/SDPMatcher.cpp:8: +/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined + #define USE_PBBAM + +: note: this is the location of the previous definition [18/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamFilter.cpp.o' -MF 'blasr_impl@sta/utils_SamFilter.cpp.o.d' -o 'blasr_impl@sta/utils_SamFilter.cpp.o' -c ../utils/SamFilter.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13, @@ -1154,8 +1188,8 @@ } catch (H5::DataSetIException e) { ^~~~~ [21/25] rm -f libblasr_impl.a && gcc-ar csrD libblasr_impl.a 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' 'blasr_impl@sta/extrautils_SAModify.cpp.o' 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' 'blasr_impl@sta/extrautils_SALS.cpp.o' 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' 'blasr_impl@sta/extrautils_Evolve.cpp.o' 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' 'blasr_impl@sta/utils_SamToM4.cpp.o' 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' 'blasr_impl@sta/utils_SDPMatcher.cpp.o' 'blasr_impl@sta/utils_LoadPulses.cpp.o' 'blasr_impl@sta/utils_PulseToFasta.cpp.o' 'blasr_impl@sta/utils_SamFilter.cpp.o' -[22/25] c++ -o sawriter 'sawriter@exe/utils_SAWriter.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libhts.so -lblasr /usr/lib/x86_64-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/build/blasr-5.3.2+dfsg/build/ -[23/25] c++ -o toAfg 'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libhts.so -lblasr /usr/lib/x86_64-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/build/blasr-5.3.2+dfsg/build/ +[22/25] c++ -o toAfg 'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libhts.so -lblasr /usr/lib/x86_64-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/build/blasr-5.3.2+dfsg/build/ +[23/25] c++ -o sawriter 'sawriter@exe/utils_SAWriter.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libhts.so -lblasr /usr/lib/x86_64-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/build/blasr-5.3.2+dfsg/build/ [24/25] c++ -Iblasr@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'blasr@exe/Blasr.cpp.o' -MF 'blasr@exe/Blasr.cpp.o.d' -o 'blasr@exe/Blasr.cpp.o' -c ../Blasr.cpp In file included from ../iblasr/BlasrHeaders.h:22, from ../iblasr/BlasrAlign.hpp:4, @@ -1242,20 +1276,22 @@ dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson -dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_5.3.2+dfsg-1.1_amd64.deb'. dpkg-deb: building package 'blasr' in '../blasr_5.3.2+dfsg-1.1_amd64.deb'. +dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_5.3.2+dfsg-1.1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../blasr_5.3.2+dfsg-1.1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/47678/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/47678/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/44749 and its subdirectories -I: Current time: Tue Aug 10 01:33:31 -12 2021 -I: pbuilder-time-stamp: 1628602411 +I: removing directory /srv/workspace/pbuilder/47678 and its subdirectories +I: Current time: Tue Sep 13 10:01:22 +14 2022 +I: pbuilder-time-stamp: 1663012882