Diff of the two buildlogs: -- --- b1/build.log 2020-08-21 23:26:32.112618481 +0000 +++ b2/build.log 2020-08-21 23:49:23.219668105 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Aug 21 10:59:14 -12 2020 -I: pbuilder-time-stamp: 1598050754 +I: Current time: Sat Aug 22 13:28:24 +14 2020 +I: pbuilder-time-stamp: 1598052504 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 Wed Sep 12 20:07:46 2018 -12 +gpgv: Signature made Thu Sep 13 22:07:46 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,136 +31,170 @@ dpkg-source: info: applying use_debian_packaged_htslib.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/18435/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/20342/tmp/hooks/D01_modify_environment starting +debug: Running on bbx15. +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/20342/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/20342/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=2' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='a43bed7eb7374fc992f9a6805ca5b9ca' - 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='18435' - PS1='# ' - PS2='> ' + INVOCATION_ID=95ae41bb1fbe4d51953c6c99fc2b17eb + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=20342 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.r3ytX8wJYm/pbuilderrc_1cgW --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.r3ytX8wJYm/b1 --logfile b1/build.log stacks_2.2+dfsg-1.dsc' - SUDO_GID='116' - SUDO_UID='112' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.r3ytX8wJYm/pbuilderrc_x9L8 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.r3ytX8wJYm/b2 --logfile b2/build.log stacks_2.2+dfsg-1.dsc' + SUDO_GID=116 + SUDO_UID=111 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux cbxi4b 4.19.0-10-armmp #1 SMP Debian 4.19.132-1 (2020-07-24) armv7l GNU/Linux + Linux i-capture-the-hostname 4.19.0-10-armmp-lpae #1 SMP Debian 4.19.132-1 (2020-07-24) armv7l GNU/Linux I: ls -l /bin total 3328 - -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 26052 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 26052 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 9636 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 22432 Feb 28 2019 cat - -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown - -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp - -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash - -rwxr-xr-x 1 root root 71648 Feb 28 2019 date - -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd - -rwxr-xr-x 1 root root 55672 Feb 28 2019 df - -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir - -rwxr-xr-x 1 root root 54872 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 22364 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 18260 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 124508 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 64232 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln - -rwxr-xr-x 1 root root 34932 Jul 26 2018 login - -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls - -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 26024 Jan 9 2019 more - -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount - -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 84284 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 22416 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm - -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 17 20:28 sh -> dash - -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty - -rwsr-xr-x 1 root root 42472 Jan 9 2019 su - -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync - -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar - -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch - -rwxr-xr-x 1 root root 18260 Feb 28 2019 true - -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount - -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 21980 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/18435/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 9636 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 22432 Mar 1 2019 cat + -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown + -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp + -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash + -rwxr-xr-x 1 root root 71648 Mar 1 2019 date + -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd + -rwxr-xr-x 1 root root 55672 Mar 1 2019 df + -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir + -rwxr-xr-x 1 root root 54872 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 22364 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 18260 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 124508 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 64232 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln + -rwxr-xr-x 1 root root 34932 Jul 27 2018 login + -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls + -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 26024 Jan 10 2019 more + -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount + -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 84284 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 22416 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm + -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 22 13:29 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 19 22:27 sh.distrib -> dash + -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty + -rwsr-xr-x 1 root root 42472 Jan 10 2019 su + -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync + -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar + -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch + -rwxr-xr-x 1 root root 18260 Mar 1 2019 true + -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount + -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 21980 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/20342/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -278,7 +312,7 @@ Get: 68 http://deb.debian.org/debian buster/main armhf libhts-dev armhf 1.9-11 [4289 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libsparsehash-dev all 2.0.2-1 [76.9 kB] Get: 70 http://deb.debian.org/debian buster/main armhf samtools armhf 1.9-4 [410 kB] -Fetched 31.0 MB in 13s (2442 kB/s) +Fetched 31.0 MB in 8s (3793 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) @@ -583,7 +617,7 @@ 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/stacks-2.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/stacks-2.2+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 stacks dpkg-buildpackage: info: source version 2.2+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -686,7 +720,7 @@ configure: WARNING: unrecognized options: --disable-maintainer-mode, --enable-sparsehash, --enable-bam, --with-bam-include-path, --with-bam-lib-path make[1]: Leaving directory '/build/stacks-2.2+dfsg' dh_auto_build - make -j3 + make -j2 make[1]: Entering directory '/build/stacks-2.2+dfsg' make all-recursive make[2]: Entering directory '/build/stacks-2.2+dfsg' @@ -695,8 +729,6 @@ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/aln_utils.o src/aln_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/BamI.o src/BamI.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/catalog_utils.o src/catalog_utils.cc -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cmb.o src/cmb.cc -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/constants.o src/constants.cc In file included from /usr/include/c++/8/vector:69, from src/constants.h:40, from src/ustacks.h:24, @@ -931,6 +963,8 @@ __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' {aka 'std::_Rb_tree_const_iterator >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cmb.o src/cmb.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/constants.o src/constants.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNANSeq.o src/DNANSeq.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq4.o src/DNASeq4.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq.o src/DNASeq.cc @@ -941,6 +975,8 @@ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/log_utils.o src/log_utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/MetaPopInfo.o src/MetaPopInfo.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/models.o src/models.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mstack.o src/mstack.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mst.o src/mst.cc In file included from /usr/include/c++/8/vector:69, from src/constants.h:40, from src/models.h:24, @@ -953,8 +989,6 @@ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mstack.o src/mstack.cc -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mst.o src/mst.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/nucleotides.o src/nucleotides.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/renz.o src/renz.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Seq.o src/Seq.cc @@ -963,7 +997,6 @@ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/utils.o src/utils.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Vcf.o src/Vcf.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks.o src/cstacks.cc -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks.o src/sstacks.cc In file included from /usr/include/c++/8/vector:69, from src/MetaPopInfo.h:5, from src/cstacks.cc:25: @@ -975,49 +1008,7 @@ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/algorithm:62, - from /usr/include/c++/8/regex:38, - from src/sstacks.cc:25: -/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, std::pair, AlignRes>&)> >]': -/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 - __unguarded_linear_insert(_RandomAccessIterator __last, - ^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, std::pair, AlignRes>&)> >]': -/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 - __insertion_sort(_RandomAccessIterator __first, - ^~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags.o src/process_radtags.cc -In file included from /usr/include/c++/8/bits/stl_algo.h:61, - from /usr/include/c++/8/algorithm:62, - from /usr/include/c++/8/regex:38, - from src/sstacks.cc:25: -/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >; _Distance = int; _Tp = std::pair, AlignRes>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, std::pair, AlignRes>&)> >]': -/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 - __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - ^~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from /usr/include/c++/8/regex:51, - from src/sstacks.cc:25: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, AlignRes>}; _Tp = std::pair, AlignRes>; _Alloc = std::allocator, AlignRes> >]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, AlignRes> >::iterator' {aka '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/map:60, - from /usr/include/c++/8/regex:52, - from src/sstacks.cc:25: -/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, AlignRes>; _KeyOfValue = std::_Select1st, AlignRes> >; _Compare = std::less >; _Alloc = std::allocator, AlignRes> >]': -/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, AlignRes>, std::_Select1st, AlignRes> >, std::less >, std::allocator, AlignRes> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, AlignRes> >'} changed in GCC 7.1 - _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks.o src/sstacks.cc In file included from /usr/include/c++/8/algorithm:62, from src/constants.h:53, from src/MetaPopInfo.h:8, @@ -1091,6 +1082,49 @@ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/c++/8/regex:38, from src/sstacks.cc:25: +/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, std::pair, AlignRes>&)> >]': +/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 + __unguarded_linear_insert(_RandomAccessIterator __last, + ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, std::pair, AlignRes>&)> >]': +/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 + __insertion_sort(_RandomAccessIterator __first, + ^~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 +In file included from /usr/include/c++/8/bits/stl_algo.h:61, + from /usr/include/c++/8/algorithm:62, + from /usr/include/c++/8/regex:38, + from src/sstacks.cc:25: +/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >; _Distance = int; _Tp = std::pair, AlignRes>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, std::pair, AlignRes>&)> >]': +/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >' changed in GCC 7.1 + __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + ^~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from /usr/include/c++/8/regex:51, + from src/sstacks.cc:25: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, AlignRes>}; _Tp = std::pair, AlignRes>; _Alloc = std::allocator, AlignRes> >]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector, AlignRes> >::iterator' {aka '__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/map:60, + from /usr/include/c++/8/regex:52, + from src/sstacks.cc:25: +/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, AlignRes>; _KeyOfValue = std::_Select1st, AlignRes> >; _Compare = std::less >; _Alloc = std::allocator, AlignRes> >]': +/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, AlignRes>, std::_Select1st, AlignRes> >, std::less >, std::allocator, AlignRes> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, AlignRes> >'} changed in GCC 7.1 + _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags.o src/process_radtags.cc +In file included from /usr/include/c++/8/algorithm:62, + from /usr/include/c++/8/regex:38, + from src/sstacks.cc:25: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, @@ -1201,7 +1235,6 @@ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter.o src/clone_filter.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations.o src/populations.cc g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/export_formats.o src/export_formats.cc -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc In file included from /usr/include/c++/8/vector:69, from src/populations.h:39, from src/populations.cc:29: @@ -1233,7 +1266,6 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/PopSum.o src/PopSum.cc In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from src/constants.h:53, @@ -1288,12 +1320,8 @@ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Hwp.o src/Hwp.cc -src/Hwp.cc: In member function 'void HWMatrix::dump_matrix()': -src/Hwp.cc:383:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=] - snprintf(buf, id_len, "%*lu ", padding, this->_g[i][j]); - ^~~~~~~~ ~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks.o src/phasedstacks.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/PopSum.o src/PopSum.cc In file included from /usr/include/c++/8/vector:69, from src/PopSum.h:26, from src/PopSum.cc:21: @@ -1305,7 +1333,6 @@ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/tsv2bam.o src/tsv2bam.cc In file included from /usr/include/c++/8/map:60, from src/PopSum.h:27, from src/PopSum.cc:21: @@ -1344,17 +1371,7 @@ __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, double> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, -In file included from /usr/include/c++/8/vector:69, - from src/phasedstacks.h:39, - from src/phasedstacks.cc:25: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Hwp.o src/Hwp.cc /usr/include/c++/8/bits/stl_map.h: In member function 'double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, double> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, @@ -1372,6 +1389,23 @@ __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, double> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, +src/Hwp.cc: In member function 'void HWMatrix::dump_matrix()': +src/Hwp.cc:383:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=] + snprintf(buf, id_len, "%*lu ", padding, this->_g[i][j]); + ^~~~~~~~ ~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks.o src/phasedstacks.cc +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/tsv2bam.o src/tsv2bam.cc +In file included from /usr/include/c++/8/vector:69, + from src/phasedstacks.h:39, + from src/phasedstacks.cc:25: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gstacks.o src/gstacks.cc src/gstacks.cc: In member function 'bool LocusProcessor::align_reads_to_contig(SuffixTree*, GappedAln*, DNASeq4&, AlignRes&) const': src/gstacks.cc:1161:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::__cxx11::basic_string::size_type' {aka 'unsigned int'} [-Wformat=] @@ -1381,31 +1415,6 @@ src/gstacks.cc:1344:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::size_t' {aka 'unsigned int'} [-Wformat=] snprintf(buf, id_len, "%luM", alns.front().aln_len); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/debruijn.o src/debruijn.cc -In file included from /usr/include/c++/8/vector:69, - from src/constants.h:40, - from src/debruijn.cc:5: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Node}; _Tp = Node; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void Graph::rebuild(const std::vector&, std::size_t)': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/SuffixTree.o src/SuffixTree.cc -rm -f libcore.a -ar cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o -ar: `u' modifier ignored since `D' is the default (see `U') -ranlib libcore.a -rm -f libclean.a -ar cru libclean.a src/clean.o src/file_io.o src/write.o -ar: `u' modifier ignored since `D' is the default (see `U') -ranlib libclean.a -rm -f libpop.a -ar cru libpop.a src/export_formats.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o -ar: `u' modifier ignored since `D' is the default (see `U') -ranlib libpop.a In file included from /usr/include/c++/8/bits/stl_algobase.h:71, from /usr/include/c++/8/vector:60, from src/constants.h:40, @@ -1416,7 +1425,6 @@ operator()(_Iterator1 __it1, _Iterator2 __it2) ^~~~~~~~ /usr/include/c++/8/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks.o -lhts libcore.a -lz -lgomp In file included from /usr/include/c++/8/algorithm:62, from src/constants.h:53, from src/gstacks.h:23, @@ -1447,11 +1455,7 @@ ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ __first + (__secondChild - 1))) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks.o -lhts libcore.a -lz -lgomp -g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks.o -lhts libcore.a -lz -lgomp -g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks.o -lhts libcore.a -lz -lgomp -g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_radtags src/process_radtags.o -lhts libcore.a libclean.a -lz -lgomp -g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_shortreads src/process_shortreads.o -lhts libcore.a libclean.a -lz -lgomp +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/debruijn.o src/debruijn.cc In file included from /usr/include/c++/8/vector:69, from src/constants.h:40, from src/gstacks.h:23, @@ -1460,22 +1464,25 @@ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o kmer_filter src/kmer_filter.o -lhts libcore.a libclean.a -lz -lgomp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 -g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o clone_filter src/clone_filter.o -lhts libcore.a libclean.a -lz -lgomp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp -g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {STAln}; _Tp = STAln; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from src/constants.h:40, + from src/debruijn.cc:5: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Node}; _Tp = Node; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {STAln}; _Tp = STAln; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -1484,8 +1491,13 @@ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc: In member function 'void Graph::rebuild(const std::vector&, std::size_t)': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 +g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/SuffixTree.o src/SuffixTree.cc In file included from /usr/include/c++/8/algorithm:62, from src/constants.h:53, from src/gstacks.h:23, @@ -1556,6 +1568,21 @@ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +rm -f libcore.a +ar cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o +ar: `u' modifier ignored since `D' is the default (see `U') +ranlib libcore.a +rm -f libclean.a +ar cru libclean.a src/clean.o src/file_io.o src/write.o +ar: `u' modifier ignored since `D' is the default (see `U') +ranlib libclean.a +rm -f libpop.a +ar cru libpop.a src/export_formats.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o +ar: `u' modifier ignored since `D' is the default (see `U') +ranlib libpop.a +g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks.o -lhts libcore.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks.o -lhts libcore.a -lz -lgomp /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, @@ -1607,6 +1634,8 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks.o -lhts libcore.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks.o -lhts libcore.a -lz -lgomp In file included from /usr/include/c++/8/vector:69, from src/constants.h:40, from src/gstacks.h:23, @@ -1622,6 +1651,11 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_radtags src/process_radtags.o -lhts libcore.a libclean.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_shortreads src/process_shortreads.o -lhts libcore.a libclean.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o kmer_filter src/kmer_filter.o -lhts libcore.a libclean.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o clone_filter src/clone_filter.o -lhts libcore.a libclean.a -lz -lgomp +g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp g++ -g -O2 -ffile-prefix-map=/build/stacks-2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o -lhts libcore.a -lz -lgomp make[3]: Leaving directory '/build/stacks-2.2+dfsg' make[2]: Leaving directory '/build/stacks-2.2+dfsg' @@ -1640,7 +1674,7 @@ dh_testroot dh_prep dh_auto_install - make -j3 install DESTDIR=/build/stacks-2.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no + make -j2 install DESTDIR=/build/stacks-2.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/stacks-2.2+dfsg' make[2]: Entering directory '/build/stacks-2.2+dfsg' make[3]: Entering directory '/build/stacks-2.2+dfsg' @@ -1667,7 +1701,7 @@ /build/stacks-2.2+dfsg/debian/tmp/usr/share/stacks/php/constants.php.dist > /build/stacks-2.2+dfsg/debian/tmp/usr/share/stacks/php/constants.php.dist.subst mv /build/stacks-2.2+dfsg/debian/tmp/usr/share/stacks/php/constants.php.dist.subst /build/stacks-2.2+dfsg/debian/tmp/usr/share/stacks/php/constants.php.dist echo 2.2 > /build/stacks-2.2+dfsg/debian/tmp/usr/share/stacks/php/version.php -/bin/bash /build/stacks-2.2+dfsg/config/install-sh -d -m 755 /build/stacks-2.2+dfsg/debian/tmp/usr/share/stacks/php/export +/bin/sh /build/stacks-2.2+dfsg/config/install-sh -d -m 755 /build/stacks-2.2+dfsg/debian/tmp/usr/share/stacks/php/export sed -i.bkp -e 's,_VERSION_,2.2,' /build/stacks-2.2+dfsg/debian/tmp/usr/bin/stacks-integrate-alignments rm -f /build/stacks-2.2+dfsg/debian/tmp/usr/bin/stacks-integrate-alignments.bkp chmod +x /build/stacks-2.2+dfsg/debian/tmp/usr/bin/stacks-integrate-alignments @@ -1718,16 +1752,16 @@ dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/tsv2bam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/populations contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/clone_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/phasedstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/sstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/kmer_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/process_radtags contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/gstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/ustacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/populations contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/process_shortreads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/process_radtags contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/phasedstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/cstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/sstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/clone_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/ustacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package stacks-web: substitution variable ${shlibs:Depends} used, but is not defined @@ -1735,21 +1769,23 @@ dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.2+dfsg-1_armhf.deb'. dpkg-deb: building package 'stacks' in '../stacks_2.2+dfsg-1_armhf.deb'. dpkg-deb: building package 'stacks-web' in '../stacks-web_2.2+dfsg-1_all.deb'. +dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.2+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../stacks_2.2+dfsg-1_armhf.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/20342/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/20342/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/18435 and its subdirectories -I: Current time: Fri Aug 21 11:26:25 -12 2020 -I: pbuilder-time-stamp: 1598052385 +I: removing directory /srv/workspace/pbuilder/20342 and its subdirectories +I: Current time: Sat Aug 22 13:49:19 +14 2020 +I: pbuilder-time-stamp: 1598053759