Diff of the two buildlogs: -- --- b1/build.log 2021-08-16 21:31:13.339662096 +0000 +++ b2/build.log 2021-08-16 21:48:15.409291903 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 16 09:27:35 -12 2021 -I: pbuilder-time-stamp: 1629149255 +I: Current time: Tue Aug 17 11:31:35 +14 2021 +I: pbuilder-time-stamp: 1629149495 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./igor_1.4.0+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.rciMt11r/trustedkeys.kbx': General error -gpgv: Signature made Wed Aug 5 04:53:54 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.p5QHvD8H/trustedkeys.kbx': General error +gpgv: Signature made Thu Aug 6 06:53:54 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,135 +31,169 @@ dpkg-source: info: applying fix-gcc-10.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/31400/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/28396/tmp/hooks/D01_modify_environment starting +debug: Running on cbxi4b. +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/28396/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/28396/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,-fixfilepath 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]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=4' + 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='c1747ab9fc334b7a99c0498eb98baa4c' - 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='31400' - PS1='# ' - PS2='> ' + INVOCATION_ID=fb5d9d9a2ad24f31b5b2bf7d6d75c2ca + 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=28396 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.RfTgmzhrrj/pbuilderrc_9pYQ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RfTgmzhrrj/b1 --logfile b1/build.log igor_1.4.0+dfsg-2.dsc' - SUDO_GID='114' - SUDO_UID='108' - 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.RfTgmzhrrj/pbuilderrc_bQou --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RfTgmzhrrj/b2 --logfile b2/build.log --extrapackages usrmerge igor_1.4.0+dfsg-2.dsc' + SUDO_GID=116 + SUDO_UID=112 + 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 virt64a 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-armmp #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more - -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 14 21:27 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/31400/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more + -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 17 11:32 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 15 23:30 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/28396/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -240,7 +274,7 @@ Get: 36 http://deb.debian.org/debian bullseye/main armhf libgsl-dev armhf 2.6+dfsg-2 [963 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libjemalloc2 armhf 5.2.1-3 [185 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf libjemalloc-dev armhf 5.2.1-3 [309 kB] -Fetched 20.2 MB in 2s (11.2 MB/s) +Fetched 20.2 MB in 3s (6302 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) @@ -409,8 +443,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (362 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 21608 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/igor-1.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../igor_1.4.0+dfsg-2_source.changes +hostname: Name or service not known +I: Running cd /build/igor-1.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../igor_1.4.0+dfsg-2_source.changes dpkg-buildpackage: info: source package igor dpkg-buildpackage: info: source version 1.4.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -449,7 +520,7 @@ ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -469,10 +540,10 @@ checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none -checking for a sed that does not truncate output... /bin/sed -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E -checking for fgrep... /bin/grep -F +checking for a sed that does not truncate output... /usr/bin/sed +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E +checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B @@ -492,8 +563,8 @@ checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no -checking for a working dd... /bin/dd -checking how to truncate binary pipes... /bin/dd bs=4096 count=1 +checking for a working dd... /usr/bin/dd +checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E @@ -563,7 +634,7 @@ === configuring in igor_src (/build/igor-1.4.0+dfsg/igor_src) configure: WARNING: no configuration information is in igor_src dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/igor-1.4.0+dfsg' make all-recursive make[2]: Entering directory '/build/igor-1.4.0+dfsg' @@ -574,6 +645,33 @@ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-CDR3SeqData.o `test -f 'CDR3SeqData.cpp' || echo './'`CDR3SeqData.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Counter.o `test -f 'Counter.cpp' || echo './'`Counter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Coverageerrcounter.o `test -f 'Coverageerrcounter.cpp' || echo './'`Coverageerrcounter.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Deletion.o `test -f 'Deletion.cpp' || echo './'`Deletion.cpp +Deletion.cpp:1590:23: warning: multi-character character constant [-Wmultichar] + 1590 | else if ((*iter)=='14'){ + | ^~~~ +Deletion.cpp: In member function 'virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': +Deletion.cpp:909:70: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: + 909 | throw invalid_argument("Unknown side for D deletion: " + (*this).event_side); //TODO explicitly throw the side used + | ^~~~~~~~~~ +Deletion.cpp:909:70: note: candidate 1: 'operator+(const char*, int)' (built-in) +In file included from Errorrate.h:29, + from Rec_Event.h:38, + from Deletion.h:29, + from Deletion.cpp:26: +Utils.h:69:13: note: candidate 2: 'std::string operator+(const string&, Seq_side)' + 69 | std::string operator+(const std::string& , Seq_side ); + | ^~~~~~~~ +Deletion.cpp:1173:67: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: + 1173 | throw invalid_argument("Unknown gene for deletions : " + this->event_class); + | ^~~~~~~~~~~ +Deletion.cpp:1173:67: note: candidate 1: 'operator+(const char*, int)' (built-in) +In file included from Errorrate.h:29, + from Rec_Event.h:38, + from Deletion.h:29, + from Deletion.cpp:26: +Utils.h:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)' + 68 | std::string operator+(const std::string& , Gene_class ); + | ^~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/queue:61, from Model_marginals.h:36, @@ -598,10 +696,11 @@ /usr/include/c++/10/bits/stl_vector.h:1249:25: note: parameter passing for argument of type 'std::vector >, std::deque >, std::allocator > > > >, std::__cxx11::list > > >::const_iterator' changed in GCC 7.1 1249 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Deletion.o `test -f 'Deletion.cpp' || echo './'`Deletion.cpp -Deletion.cpp:1590:23: warning: multi-character character constant [-Wmultichar] - 1590 | else if ((*iter)=='14'){ - | ^~~~ +Deletion.cpp: In member function 'virtual bool Deletion::has_effect_on(Seq_type) const': +Deletion.cpp:1705:2: warning: control reaches end of non-void function [-Wreturn-type] + 1705 | } + | ^ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Dinuclmarkov.o `test -f 'Dinuclmarkov.cpp' || echo './'`Dinuclmarkov.cpp In file included from /usr/include/c++/10/bits/stl_algobase.h:71, from /usr/include/c++/10/bits/forward_list.h:38, from /usr/include/c++/10/forward_list:38, @@ -612,51 +711,7 @@ 155 | operator()(_Iterator1 __it1, _Iterator2 __it2) | ^~~~~~~~ /usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -Deletion.cpp: In member function 'virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': -Deletion.cpp:909:70: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: - 909 | throw invalid_argument("Unknown side for D deletion: " + (*this).event_side); //TODO explicitly throw the side used - | ^~~~~~~~~~ -Deletion.cpp:909:70: note: candidate 1: 'operator+(const char*, int)' (built-in) -In file included from Errorrate.h:29, - from Rec_Event.h:38, - from Deletion.h:29, - from Deletion.cpp:26: -Utils.h:69:13: note: candidate 2: 'std::string operator+(const string&, Seq_side)' - 69 | std::string operator+(const std::string& , Seq_side ); - | ^~~~~~~~ -Deletion.cpp:1173:67: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: - 1173 | throw invalid_argument("Unknown gene for deletions : " + this->event_class); - | ^~~~~~~~~~~ -Deletion.cpp:1173:67: note: candidate 1: 'operator+(const char*, int)' (built-in) -In file included from Errorrate.h:29, - from Rec_Event.h:38, - from Deletion.h:29, - from Deletion.cpp:26: -Utils.h:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)' - 68 | std::string operator+(const std::string& , Gene_class ); - | ^~~~~~~~ -Deletion.cpp: In member function 'virtual bool Deletion::has_effect_on(Seq_type) const': -Deletion.cpp:1705:2: warning: control reaches end of non-void function [-Wreturn-type] - 1705 | } - | ^ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Dinuclmarkov.o `test -f 'Dinuclmarkov.cpp' || echo './'`Dinuclmarkov.cpp -In file included from /usr/include/c++/10/vector:72, - from Utils.h:31, - from Aligner.h:37, - from Aligner.cpp:27: -/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/10/bits/vector.tcc: In function 'Matrix read_substitution_matrix(const string&, std::string)': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Alignment_data}; _Tp = Alignment_data; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorscounter.o `test -f 'Errorscounter.cpp' || echo './'`Errorscounter.cpp Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate(double&, Downstream_scenario_proba_bound_map&, const string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Dinuclmarkov.cpp:147:81: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 147 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); @@ -681,10 +736,6 @@ Utils.h:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In function 'std::unordered_map > read_alignments_seq_csv(std::string, double, bool)': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate_initialize_Len_proba(Seq_type, std::map&, std::queue >&, double&, const Marginal_array_p&, Index_map&, Seq_type_str_p_map&, int&) const': Dinuclmarkov.cpp:565:81: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 565 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class); @@ -705,6 +756,53 @@ Utils.h:142:2: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ +In file included from /usr/include/c++/10/vector:72, + from Utils.h:31, + from Aligner.h:37, + from Aligner.cpp:27: +/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/10/bits/vector.tcc: In function 'Matrix read_substitution_matrix(const string&, std::string)': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from /usr/include/c++/10/queue:61, + from Model_marginals.h:36, + from Counter.h:32, + from Errorscounter.h:29, + from Errorscounter.cpp:26: +/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_emplace_aux(std::vector<_Tp, _Alloc>::const_iterator, _Args&& ...) [with _Args = {long double&, unsigned int&, unsigned int&}; _Tp = std::tuple; _Alloc = std::allocator >]': +/usr/include/c++/10/bits/vector.tcc:364:7: note: parameter passing for argument of type 'std::vector >::const_iterator' changed in GCC 7.1 + 364 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from /usr/include/c++/10/queue:61, + from Model_marginals.h:36, + from Counter.h:32, + from Errorscounter.h:29, + from Errorscounter.cpp:26: +/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void Errors_counter::count_scenario(long double, double, const string&, Seq_type_str_p_map&, const Seq_offsets_map&, const std::unordered_map, std::shared_ptr >&, Mismatch_vectors_map&)': +/usr/include/c++/10/bits/stl_vector.h:1249:25: note: parameter passing for argument of type 'std::vector >::const_iterator' changed in GCC 7.1 + 1249 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); } + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:1249:25: note: parameter passing for argument of type 'std::vector >::const_iterator' changed in GCC 7.1 + 1249 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); } + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Alignment_data}; _Tp = Alignment_data; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorrate.o `test -f 'Errorrate.cpp' || echo './'`Errorrate.cpp +/usr/include/c++/10/bits/vector.tcc: In function 'std::unordered_map > read_alignments_seq_csv(std::string, double, bool)': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-ExtractFeatures.o `test -f 'ExtractFeatures.cpp' || echo './'`ExtractFeatures.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.cpp In file included from /usr/include/c++/10/algorithm:62, from Aligner.h:35, from Aligner.cpp:27: @@ -712,11 +810,24 @@ /usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-GenModel.o `test -f 'GenModel.cpp' || echo './'`GenModel.cpp /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +Genechoice.cpp: In member function 'virtual void Gene_choice::iterate(double&, Downstream_scenario_proba_bound_map&, const string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': +Genechoice.cpp:908:73: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: + 908 | throw invalid_argument("Unknown gene_class for GeneChoice: " + this->event_class); + | ^~~~~~~~~~~ +Genechoice.cpp:908:73: note: candidate 1: 'operator+(const char*, int)' (built-in) +In file included from Errorrate.h:29, + from Rec_Event.h:38, + from Genechoice.h:29, + from Genechoice.cpp:26: +Utils.h:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)' + 68 | std::string operator+(const std::string& , Gene_class ); + | ^~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, @@ -760,7 +871,6 @@ | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorscounter.o `test -f 'Errorscounter.cpp' || echo './'`Errorscounter.cpp /usr/include/c++/10/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]': /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, @@ -793,45 +903,6 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorrate.o `test -f 'Errorrate.cpp' || echo './'`Errorrate.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-ExtractFeatures.o `test -f 'ExtractFeatures.cpp' || echo './'`ExtractFeatures.cpp -In file included from /usr/include/c++/10/vector:72, - from /usr/include/c++/10/queue:61, - from Model_marginals.h:36, - from Counter.h:32, - from Errorscounter.h:29, - from Errorscounter.cpp:26: -/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_emplace_aux(std::vector<_Tp, _Alloc>::const_iterator, _Args&& ...) [with _Args = {long double&, unsigned int&, unsigned int&}; _Tp = std::tuple; _Alloc = std::allocator >]': -/usr/include/c++/10/bits/vector.tcc:364:7: note: parameter passing for argument of type 'std::vector >::const_iterator' changed in GCC 7.1 - 364 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from /usr/include/c++/10/queue:61, - from Model_marginals.h:36, - from Counter.h:32, - from Errorscounter.h:29, - from Errorscounter.cpp:26: -/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void Errors_counter::count_scenario(long double, double, const string&, Seq_type_str_p_map&, const Seq_offsets_map&, const std::unordered_map, std::shared_ptr >&, Mismatch_vectors_map&)': -/usr/include/c++/10/bits/stl_vector.h:1249:25: note: parameter passing for argument of type 'std::vector >::const_iterator' changed in GCC 7.1 - 1249 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); } - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:1249:25: note: parameter passing for argument of type 'std::vector >::const_iterator' changed in GCC 7.1 - 1249 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); } - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-GenModel.o `test -f 'GenModel.cpp' || echo './'`GenModel.cpp -Genechoice.cpp: In member function 'virtual void Gene_choice::iterate(double&, Downstream_scenario_proba_bound_map&, const string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': -Genechoice.cpp:908:73: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: - 908 | throw invalid_argument("Unknown gene_class for GeneChoice: " + this->event_class); - | ^~~~~~~~~~~ -Genechoice.cpp:908:73: note: candidate 1: 'operator+(const char*, int)' (built-in) -In file included from Errorrate.h:29, - from Rec_Event.h:38, - from Genechoice.h:29, - from Genechoice.cpp:26: -Utils.h:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)' - 68 | std::string operator+(const std::string& , Gene_class ); - | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-HypermutationfullNmererrorrate.o `test -f 'HypermutationfullNmererrorrate.cpp' || echo './'`HypermutationfullNmererrorrate.cpp In file included from /usr/include/c++/10/vector:72, from Rec_Event.h:32, @@ -841,6 +912,7 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector, std::allocator >, int, int, double> >::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Hypermutationglobalerrorrate.o `test -f 'Hypermutationglobalerrorrate.cpp' || echo './'`Hypermutationglobalerrorrate.cpp In file included from Errorrate.h:29, from HypermutationfullNmererrorrate.h:30, from HypermutationfullNmererrorrate.cpp:27: @@ -848,36 +920,6 @@ Utils.h:142:2: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ -In file included from /usr/include/c++/10/vector:72, - from Rec_Event.h:32, - from Model_Parms.h:33, - from GenModel.h:32, - from GenModel.cpp:28: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Alignment_data&}; _Tp = Alignment_data; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from Rec_Event.h:32, - from Model_Parms.h:33, - from GenModel.h:32, - from GenModel.cpp:28: -/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector, std::allocator >, std::unordered_map >, std::hash, std::equal_to, std::allocator > > > > > > get_best_aligns(const std::vector, std::allocator >, std::unordered_map >, std::hash, std::equal_to, std::allocator > > > > > >&, Gene_class)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/algorithm:62, - from Aligner.h:35, - from Rec_Event.h:41, - from Genechoice.h:29, - from Genechoice.cpp:26: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 - 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, - | ^~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 In file included from /usr/include/c++/10/queue:62, from Errorrate.h:38, from HypermutationfullNmererrorrate.h:30, @@ -906,10 +948,6 @@ /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 - 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1881 | __final_insertion_sort(_RandomAccessIterator __first, @@ -921,30 +959,18 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 - 1839 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 -In file included from /usr/include/c++/10/queue:62, - from Rec_Event.h:37, - from Genechoice.h:29, - from Genechoice.cpp:26: -/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Distance = int; _Tp = std::tuple, std::allocator >, int, int, double>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 - 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from Aligner.h:35, from Rec_Event.h:41, from Genechoice.h:29, from Genechoice.cpp:26: -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 - 1662 | __heap_select(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 + 79 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, + | ^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 In file included from /usr/include/c++/10/vector:72, from Utils.h:31, from Errorrate.h:29, @@ -1004,24 +1030,10 @@ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 - 1945 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 - 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1925 | __comp); - | ~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 -/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 - 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 - 1937 | std::__heap_select(__first, __middle, __last, __comp); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 + 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from Utils.h:31, from Errorrate.h:29, @@ -1047,6 +1059,73 @@ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 + 1839 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 +In file included from /usr/include/c++/10/vector:72, + from Rec_Event.h:32, + from Model_Parms.h:33, + from GenModel.h:32, + from GenModel.cpp:28: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Alignment_data&}; _Tp = Alignment_data; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from Errorrate.h:29, + from Hypermutationglobalerrorrate.h:30, + from Hypermutationglobalerrorrate.cpp:27: +Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': +Utils.h:142:2: warning: control reaches end of non-void function [-Wreturn-type] + 142 | } + | ^ +In file included from /usr/include/c++/10/queue:62, + from Rec_Event.h:37, + from Genechoice.h:29, + from Genechoice.cpp:26: +/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Distance = int; _Tp = std::tuple, std::allocator >, int, int, double>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 + 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/10/algorithm:62, + from Aligner.h:35, + from Rec_Event.h:41, + from Genechoice.h:29, + from Genechoice.cpp:26: +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 + 1662 | __heap_select(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 + 1945 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 + 1924 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1925 | __comp); + | ~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 + 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 + 1937 | std::__heap_select(__first, __middle, __last, __comp); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from Rec_Event.h:32, + from Model_Parms.h:33, + from GenModel.h:32, + from GenModel.cpp:28: +/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector, std::allocator >, std::unordered_map >, std::hash, std::equal_to, std::allocator > > > > > > get_best_aligns(const std::vector, std::allocator >, std::unordered_map >, std::hash, std::equal_to, std::allocator > > > > > >&, Gene_class)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from Rec_Event.h:32, from Genechoice.h:29, @@ -1073,15 +1152,9 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, std::allocator >, int, int, double>*, std::vector, std::allocator >, int, int, double> > >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Hypermutationglobalerrorrate.o `test -f 'Hypermutationglobalerrorrate.cpp' || echo './'`Hypermutationglobalerrorrate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Insertion.o `test -f 'Insertion.cpp' || echo './'`Insertion.cpp -In file included from Errorrate.h:29, - from Hypermutationglobalerrorrate.h:30, - from Hypermutationglobalerrorrate.cpp:27: -Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': -Utils.h:142:2: warning: control reaches end of non-void function [-Wreturn-type] - 142 | } - | ^ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-IntStr.o `test -f 'IntStr.cpp' || echo './'`IntStr.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_marginals.o `test -f 'Model_marginals.cpp' || echo './'`Model_marginals.cpp Insertion.cpp: In member function 'virtual void Insertion::iterate(double&, Downstream_scenario_proba_bound_map&, const string&, const Int_Str&, Index_map&, const std::unordered_map, std::vector, int> > >&, std::shared_ptr&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr&, std::map >&, const std::unordered_map, std::shared_ptr >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)': Insertion.cpp:244:72: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second: 244 | throw invalid_argument("Unknown gene_class for Insertion: " + this->event_class); @@ -1094,8 +1167,6 @@ Utils.h:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)' 68 | std::string operator+(const std::string& , Gene_class ); | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-IntStr.o `test -f 'IntStr.cpp' || echo './'`IntStr.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_marginals.o `test -f 'Model_marginals.cpp' || echo './'`Model_marginals.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_Parms.o `test -f 'Model_Parms.cpp' || echo './'`Model_Parms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Pgencounter.o `test -f 'Pgencounter.cpp' || echo './'`Pgencounter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Rec_Event.o `test -f 'Rec_Event.cpp' || echo './'`Rec_Event.cpp @@ -1107,6 +1178,15 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp +In file included from Errorrate.h:29, + from Singleerrorrate.h:30, + from Singleerrorrate.cpp:27: +Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': +Utils.h:142:2: warning: control reaches end of non-void function [-Wreturn-type] + 142 | } + | ^ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.cpp /usr/include/c++/10/bits/vector.tcc: In member function 'void Model_Parms::read_model_parms(std::string)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -1120,15 +1200,6 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp -In file included from Errorrate.h:29, - from Singleerrorrate.h:30, - from Singleerrorrate.cpp:27: -Utils.h: In member function 'Matrix& Matrix::operator=(const Matrix&) [with T = double]': -Utils.h:142:2: warning: control reaches end of non-void function [-Wreturn-type] - 142 | } - | ^ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.cpp main.cpp: In function 'int main(int, char**)': main.cpp:257:10: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -1166,7 +1237,7 @@ Utils.h:142:2: warning: control reaches end of non-void function [-Wreturn-type] 142 | } | ^ -/bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl +/bin/sh ../libtool --tag=CXX --mode=link g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl libtool: link: g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl -fopenmp make[3]: Leaving directory '/build/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/igor-1.4.0+dfsg' @@ -1174,7 +1245,7 @@ make[2]: Leaving directory '/build/igor-1.4.0+dfsg' make[1]: Leaving directory '/build/igor-1.4.0+dfsg' dh_auto_test - make -j3 check VERBOSE=1 + make -j4 check VERBOSE=1 make[1]: Entering directory '/build/igor-1.4.0+dfsg' Making check in igor_src make[2]: Entering directory '/build/igor-1.4.0+dfsg/igor_src' @@ -1192,19 +1263,19 @@ Making install in igor_src make[2]: Entering directory '/build/igor-1.4.0+dfsg/igor_src' make[3]: Entering directory '/build/igor-1.4.0+dfsg/igor_src' - /bin/mkdir -p '/build/igor-1.4.0+dfsg/debian/igor/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c igor '/build/igor-1.4.0+dfsg/debian/igor/usr/bin' + /usr/bin/mkdir -p '/build/igor-1.4.0+dfsg/debian/igor/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c igor '/build/igor-1.4.0+dfsg/debian/igor/usr/bin' libtool: install: /usr/bin/install -c igor /build/igor-1.4.0+dfsg/debian/igor/usr/bin/igor make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/igor-1.4.0+dfsg/igor_src' make[2]: Leaving directory '/build/igor-1.4.0+dfsg/igor_src' make[2]: Entering directory '/build/igor-1.4.0+dfsg' make[3]: Entering directory '/build/igor-1.4.0+dfsg' - /bin/mkdir -p '/build/igor-1.4.0+dfsg/debian/igor/usr/bin' + /usr/bin/mkdir -p '/build/igor-1.4.0+dfsg/debian/igor/usr/bin' /usr/bin/install -c scripts/igor-compute_pgen '/build/igor-1.4.0+dfsg/debian/igor/usr/bin' mkdir -p /build/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models cp -r models/* /build/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models - /bin/mkdir -p '/build/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo' + /usr/bin/mkdir -p '/build/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo' /usr/bin/install -c -m 644 demo/genomicVs_with_primers.fasta demo/genomicDs.fasta demo/genomicJs_all_curated.fasta demo/murugan_naive1_noncoding_demo_seqs.txt '/build/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo' make[3]: Leaving directory '/build/igor-1.4.0+dfsg' make[2]: Leaving directory '/build/igor-1.4.0+dfsg' @@ -1246,12 +1317,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/28396/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/28396/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/31400 and its subdirectories -I: Current time: Mon Aug 16 09:31:09 -12 2021 -I: pbuilder-time-stamp: 1629149469 +I: removing directory /srv/workspace/pbuilder/28396 and its subdirectories +I: Current time: Tue Aug 17 11:48:11 +14 2021 +I: pbuilder-time-stamp: 1629150491