Diff of the two buildlogs: -- --- b1/build.log 2023-05-26 16:45:17.150728599 +0000 +++ b2/build.log 2023-05-26 17:42:52.083273172 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 26 03:56:59 -12 2023 -I: pbuilder-time-stamp: 1685116619 +I: Current time: Sat May 27 06:45:33 +14 2023 +I: pbuilder-time-stamp: 1685119533 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./augustus_3.5.0+dfsg.orig.tar.xz] I: copying [./augustus_3.5.0+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Nov 20 11:29:04 2022 -12 +gpgv: Signature made Mon Nov 21 13:29:04 2022 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./augustus_3.5.0+dfsg-2.dsc: no acceptable signature found @@ -32,135 +32,167 @@ dpkg-source: info: applying s390x-disable-filterbam-tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3382/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/10065/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 27 06:47 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/10065/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/10065/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='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='f68f6fe013544e93a8fa54b5464f1062' - 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='3382' - PS1='# ' - PS2='> ' + INVOCATION_ID=38a7cb1a2a414d4fa4ad48efcb275a1c + 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=10065 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.XBBQ33f6/pbuilderrc_uUGJ --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XBBQ33f6/b1 --logfile b1/build.log augustus_3.5.0+dfsg-2.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.XBBQ33f6/pbuilderrc_fbz9 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XBBQ33f6/b2 --logfile b2/build.log --extrapackages usrmerge augustus_3.5.0+dfsg-2.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64c 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/3382/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 27 06:47 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/10065/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -358,7 +390,7 @@ Get: 128 http://deb.debian.org/debian bookworm/main armhf libncurses5-dev armhf 6.4-4 [932 B] Get: 129 http://deb.debian.org/debian bookworm/main armhf libsqlite3-dev armhf 3.40.1-2 [926 kB] Get: 130 http://deb.debian.org/debian bookworm/main armhf samtools armhf 1.16.1-1 [575 kB] -Fetched 70.9 MB in 1s (47.8 MB/s) +Fetched 70.9 MB in 4s (19.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 19326 files and directories currently installed.) @@ -907,8 +939,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/augustus-3.5.0+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 > ../augustus_3.5.0+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/10065/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/10065/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/augustus-3.5.0+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 > ../augustus_3.5.0+dfsg-2_source.changes dpkg-buildpackage: info: source package augustus dpkg-buildpackage: info: source version 3.5.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -1099,15 +1142,18 @@ cp -f joingenes ../../bin/ make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/joingenes' dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/augustus-3.5.0+dfsg' mkdir -p bin -mkdir -p bin cd src && make -cd auxprogs && make +mkdir -p bin make[3]: Entering directory '/build/augustus-3.5.0+dfsg/src' +cd auxprogs && make +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs' cd aln2wig; make; +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o properties.o properties.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_profile.o pp_profile.cc make[4]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/aln2wig' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'aln2wig' is up to date. @@ -1118,8 +1164,6 @@ make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2hints' cd compileSpliceCands; make; -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o properties.o properties.cc make[4]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Nothing to be done for 'all'. @@ -1252,105 +1296,6 @@ src/Coord_Transform.cpp:65:13: note: 'skip_end' was declared here 65 | int skip_end; //normally end position + W for this next intron | ^~~~~~~~ -Finished building: src/Coord_Transform.cpp - -Building file: src/Genomic_Data.cpp -Invoking: GCC C++ Compiler: g++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Genomic_Data.d" -MT"build/Genomic_Data.o" -o "build/Genomic_Data.o" "src/Genomic_Data.cpp" -In file included from /usr/include/c++/12/map:60, - from ../include/types.hh:39, - from ../include/properties.hh:14, - from properties.cc:8: -/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st, nlohmann::basic_json<> > >; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]': -/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 - 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st, nlohmann::basic_json<> > >; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61: -/usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = nlohmann::basic_json<>; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]': -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = nlohmann::basic_json<>; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]', - inlined from 'bool nlohmann::detail::json_sax_dom_callback_parser::key(string_t&) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5599:76: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from ../include/types.hh:36: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', - inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = nlohmann::detail::value_t; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, - inlined from 'bool nlohmann::detail::json_sax_dom_parser::start_array(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5423:41: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', - inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = nlohmann::detail::value_t; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, - inlined from 'bool nlohmann::detail::json_sax_dom_parser::start_object(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5397:41: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/12/bits/stl_algobase.h:64, - from /usr/include/c++/12/string:50, - from src/Genomic_Data.hpp:8, - from src/Genomic_Data.cpp:5: -In constructor 'constexpr std::pair<_T1, _T2>::pair(_U1&&, _U2&&) [with _U1 = unsigned int&; _U2 = unsigned int&; typename std::enable_if<(std::_PCC::_MoveConstructiblePair<_U1, _U2>() && std::_PCC::_ImplicitlyMoveConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]', - inlined from 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = unsigned int&; _T2 = unsigned int&]' at /usr/include/c++/12/bits/stl_pair.h:746:72, - inlined from 'std::vector > lower_case_runs(std::string)' at src/Genomic_Data.cpp:62:19: -/usr/include/c++/12/bits/stl_pair.h:535:11: warning: 'start' may be used uninitialized [-Wmaybe-uninitialized] - 535 | : first(std::forward<_U1>(__x)), second(std::forward<_U2>(__y)) { } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/Genomic_Data.cpp: In function 'std::vector > lower_case_runs(std::string)': -src/Genomic_Data.cpp:42:18: note: 'start' was declared here - 42 | unsigned start; - | ^~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', - inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = std::__cxx11::basic_string&; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, - inlined from 'bool nlohmann::detail::json_sax_dom_parser::string(string_t&) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5385:21, - inlined from 'bool nlohmann::detail::parser::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser >; BasicJsonType = nlohmann::basic_json<>; InputAdapterType = nlohmann::detail::input_stream_adapter]' at ../include/json.hpp:10428:29: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', - inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = long long unsigned int&; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, - inlined from 'bool nlohmann::detail::json_sax_dom_parser::number_unsigned(number_unsigned_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5373:21, - inlined from 'bool nlohmann::detail::parser::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser >; BasicJsonType = nlohmann::basic_json<>; InputAdapterType = nlohmann::detail::input_stream_adapter]' at ../include/json.hpp:10437:29: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_profile.o pp_profile.cc -Finished building: src/Genomic_Data.cpp - -Building file: src/Splice_Sites.cpp -Invoking: GCC C++ Compiler: g++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Splice_Sites.d" -MT"build/Splice_Sites.o" -o "build/Splice_Sites.o" "src/Splice_Sites.cpp" -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_hitseq.o pp_hitseq.cc -Finished building: src/Splice_Sites.cpp - -Building file: src/Supporting_Methods.cpp -Invoking: GCC C++ Compiler: g++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Supporting_Methods.d" -MT"build/Supporting_Methods.o" -o "build/Supporting_Methods.o" "src/Supporting_Methods.cpp" In file included from /usr/include/c++/12/vector:70, from ../include/types.hh:36, from ../include/geneticcode.hh:12, @@ -1366,7 +1311,11 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_scoring.o pp_scoring.cc +Finished building: src/Coord_Transform.cpp + +Building file: src/Genomic_Data.cpp +Invoking: GCC C++ Compiler: g++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Genomic_Data.d" -MT"build/Genomic_Data.o" -o "build/Genomic_Data.o" "src/Genomic_Data.cpp" /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: @@ -1375,11 +1324,6 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -Finished building: src/Supporting_Methods.cpp - -Building file: src/Test.cpp -Invoking: GCC C++ Compiler: g++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Test.d" -MT"build/Test.o" -o "build/Test.o" "src/Test.cpp" /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]', @@ -1443,11 +1387,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -Finished building: src/Test.cpp - -Building file: src/UTRs.cpp -Invoking: GCC C++ Compiler: g++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/UTRs.d" -MT"build/UTRs.o" -o "build/UTRs.o" "src/UTRs.cpp" /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {PP::Block}; _Tp = PP::Block; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -1458,98 +1397,102 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -src/UTRs.cpp:83:9: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 83 | binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, +In file included from /usr/include/c++/12/map:60, + from ../include/types.hh:39, + from ../include/properties.hh:14, + from properties.cc:8: +/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st, nlohmann::basic_json<> > >; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]': +/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 + 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st, nlohmann::basic_json<> > >; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: +/usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = nlohmann::basic_json<>; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]': +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = nlohmann::basic_json<>; _Compare = std::less >; _Alloc = std::allocator, nlohmann::basic_json<> > >]', + inlined from 'bool nlohmann::detail::json_sax_dom_callback_parser::key(string_t&) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5599:76: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, nlohmann::basic_json<> >, std::_Select1st, nlohmann::basic_json<> > >, std::less >, std::allocator, nlohmann::basic_json<> > > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_hitseq.o pp_hitseq.cc +In file included from /usr/include/c++/12/vector:70, + from ../include/types.hh:36: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', + inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = nlohmann::detail::value_t; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, + inlined from 'bool nlohmann::detail::json_sax_dom_parser::start_array(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5423:41: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', + inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = nlohmann::detail::value_t; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, + inlined from 'bool nlohmann::detail::json_sax_dom_parser::start_object(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5397:41: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/12/bits/stl_algobase.h:64, + from /usr/include/c++/12/string:50, from src/Genomic_Data.hpp:8, - from src/UTRs.cpp:5: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -src/UTRs.cpp:92:9: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 92 | binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -src/UTRs.cpp:100:59: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 100 | template struct finding_intron_greater_s : binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -src/UTRs.cpp:108:58: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 108 | template struct finding_intron_lesser_s : binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -src/UTRs.cpp:116:59: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 116 | template struct finding_intron_greater_e : binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -src/UTRs.cpp:124:58: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 124 | template struct finding_intron_lesser_e : binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -src/UTRs.cpp:133:49: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 133 | template struct finding_repeat : binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -src/UTRs.cpp: In static member function 'static unsigned int UTRs::get_max_pos(unsigned int, int, unsigned int, unsigned int, std::vector*)': -src/UTRs.cpp:181:64: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_coding_region_greater; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 181 | bind2nd(finding_coding_region_greater(), pos)) : - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_function.h:1438: -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -src/UTRs.cpp:183:65: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_coding_region_lesser; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 183 | bind2nd(finding_coding_region_lesser(), pos)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -src/UTRs.cpp: In static member function 'static bool UTRs::repeat_in_UTR(unsigned int, unsigned int, std::vector*)': -src/UTRs.cpp:196:63: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_repeat; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 196 | it = find_if(repeats->begin(), repeats->end(), bind2nd(finding_repeat(), start)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -src/UTRs.cpp: In static member function 'static std::vector UTRs::find_introns_in_range(unsigned int, unsigned int, int, std::vector*)': -src/UTRs.cpp:233:79: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_s; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 233 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_s(), start)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -src/UTRs.cpp:240:79: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_e; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 240 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_e(), start)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -src/UTRs.cpp:252:93: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_e; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 252 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_e(), start)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -src/UTRs.cpp:259:93: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_s; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 259 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_s(), start)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ + from src/Genomic_Data.cpp:5: +In constructor 'constexpr std::pair<_T1, _T2>::pair(_U1&&, _U2&&) [with _U1 = unsigned int&; _U2 = unsigned int&; typename std::enable_if<(std::_PCC::_MoveConstructiblePair<_U1, _U2>() && std::_PCC::_ImplicitlyMoveConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]', + inlined from 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = unsigned int&; _T2 = unsigned int&]' at /usr/include/c++/12/bits/stl_pair.h:746:72, + inlined from 'std::vector > lower_case_runs(std::string)' at src/Genomic_Data.cpp:62:19: +/usr/include/c++/12/bits/stl_pair.h:535:11: warning: 'start' may be used uninitialized [-Wmaybe-uninitialized] + 535 | : first(std::forward<_U1>(__x)), second(std::forward<_U2>(__y)) { } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +src/Genomic_Data.cpp: In function 'std::vector > lower_case_runs(std::string)': +src/Genomic_Data.cpp:42:18: note: 'start' was declared here + 42 | unsigned start; + | ^~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_scoring.o pp_scoring.cc +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', + inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = std::__cxx11::basic_string&; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, + inlined from 'bool nlohmann::detail::json_sax_dom_parser::string(string_t&) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5385:21, + inlined from 'bool nlohmann::detail::parser::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser >; BasicJsonType = nlohmann::basic_json<>; InputAdapterType = nlohmann::detail::input_stream_adapter]' at ../include/json.hpp:10428:29: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]', + inlined from 'BasicJsonType* nlohmann::detail::json_sax_dom_parser::handle_value(Value&&) [with Value = long long unsigned int&; BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5479:58, + inlined from 'bool nlohmann::detail::json_sax_dom_parser::number_unsigned(number_unsigned_t) [with BasicJsonType = nlohmann::basic_json<>]' at ../include/json.hpp:5373:21, + inlined from 'bool nlohmann::detail::parser::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser >; BasicJsonType = nlohmann::basic_json<>; InputAdapterType = nlohmann::detail::input_stream_adapter]' at ../include/json.hpp:10437:29: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o statemodel.o statemodel.cc +Finished building: src/Genomic_Data.cpp + +Building file: src/Splice_Sites.cpp +Invoking: GCC C++ Compiler: g++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Splice_Sites.d" -MT"build/Splice_Sites.o" -o "build/Splice_Sites.o" "src/Splice_Sites.cpp" +Finished building: src/Splice_Sites.cpp + +Building file: src/Supporting_Methods.cpp +Invoking: GCC C++ Compiler: g++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Supporting_Methods.d" -MT"build/Supporting_Methods.o" -o "build/Supporting_Methods.o" "src/Supporting_Methods.cpp" +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.cc In file included from /usr/include/c++/12/vector:70, from ../include/types.hh:36, from ../include/vitmatrix.hh:12, @@ -1577,6 +1520,11 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +Finished building: src/Supporting_Methods.cpp + +Building file: src/Test.cpp +Invoking: GCC C++ Compiler: g++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Test.d" -MT"build/Test.o" -o "build/Test.o" "src/Test.cpp" /usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: @@ -1681,6 +1629,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 926 | std::forward<_Pair>(__x)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from ../include/matrix.hh:12, + from ../include/statemodel.hh:12, + from statemodel.cc:8: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Ancestor; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void StateModel::initPredecessors(Matrix&, int)' at statemodel.cc:45:24: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_map.h:1137:26, inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15, @@ -1709,12 +1671,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from src/Genomic_Data.hpp:9: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +Finished building: src/Test.cpp + +Building file: src/UTRs.cpp +Invoking: GCC C++ Compiler: g++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/UTRs.d" -MT"build/UTRs.o" -o "build/UTRs.o" "src/UTRs.cpp" In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::erase(const_iterator, const_iterator) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_map.h:1137:26, inlined from 'void ViterbiSubmapType::erase(iterator, iterator) const' at ../include/vitmatrix.hh:329:15, @@ -1732,37 +1693,99 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from ../include/matrix.hh:12, - from ../include/statemodel.hh:12, - from statemodel.cc:8: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Ancestor; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void StateModel::initPredecessors(Matrix&, int)' at statemodel.cc:45:24: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void boost::assign_detail::call_push_back::operator()(T&&) [with T = double; C = std::vector >]' at /usr/include/boost/assign/list_inserter.hpp:91:25, - inlined from 'void boost::assign::list_inserter::insert(single_arg_type, T&&) [with T = double; Function = boost::assign_detail::call_push_back > >; Argument = double]' at /usr/include/boost/assign/list_inserter.hpp:414:20, - inlined from 'boost::assign::list_inserter& boost::assign::list_inserter::operator()(Ts&& ...) [with Ts = {double}; Function = boost::assign_detail::call_push_back > >; Argument = double]' at /usr/include/boost/assign/list_inserter.hpp:406:19, - inlined from 'boost::assign::list_inserter >, V> boost::assign::operator+=(std::vector<_Tp, _Alloc>&, V2&&) [with V = double; A = std::allocator; V2 = double]' at /usr/include/boost/assign/std/vector.hpp:42:30, - inlined from 'static void UTRs::compute_UTRs(const Genomic_Data::Scaff_plus_Gen_Data&, const std::map&)' at src/UTRs.cpp:382:7: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o types.o types.cc -Finished building: src/UTRs.cpp - -Building file: src/main.cpp -Invoking: GCC C++ Compiler: g++ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/main.d" -MT"build/main.o" -o "build/main.o" "src/main.cpp" +src/UTRs.cpp:83:9: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 83 | binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from src/Genomic_Data.hpp:8, + from src/UTRs.cpp:5: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +src/UTRs.cpp:92:9: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 92 | binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +src/UTRs.cpp:100:59: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 100 | template struct finding_intron_greater_s : binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +src/UTRs.cpp:108:58: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 108 | template struct finding_intron_lesser_s : binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +src/UTRs.cpp:116:59: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 116 | template struct finding_intron_greater_e : binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +src/UTRs.cpp:124:58: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 124 | template struct finding_intron_lesser_e : binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +src/UTRs.cpp:133:49: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 133 | template struct finding_repeat : binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +src/UTRs.cpp: In static member function 'static unsigned int UTRs::get_max_pos(unsigned int, int, unsigned int, unsigned int, std::vector*)': +src/UTRs.cpp:181:64: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_coding_region_greater; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 181 | bind2nd(finding_coding_region_greater(), pos)) : + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_function.h:1438: +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +src/UTRs.cpp:183:65: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_coding_region_lesser; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 183 | bind2nd(finding_coding_region_lesser(), pos)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +src/UTRs.cpp: In static member function 'static bool UTRs::repeat_in_UTR(unsigned int, unsigned int, std::vector*)': +src/UTRs.cpp:196:63: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_repeat; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 196 | it = find_if(repeats->begin(), repeats->end(), bind2nd(finding_repeat(), start)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +src/UTRs.cpp: In static member function 'static std::vector UTRs::find_introns_in_range(unsigned int, unsigned int, int, std::vector*)': +src/UTRs.cpp:233:79: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_s; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 233 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_s(), start)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +src/UTRs.cpp:240:79: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_e; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 240 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_e(), start)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +src/UTRs.cpp:252:93: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_e; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 252 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_e(), start)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +src/UTRs.cpp:259:93: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_s; _Tp = unsigned int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 259 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_s(), start)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o gene.o gene.cc In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from ../include/types.hh:38, @@ -1808,21 +1831,6 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -Finished building: src/main.cpp - -Building target: utrrnaseq -Invoking: GCC C++ Linker -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o utrrnaseq build/Compute_UTRs.o build/Coord_Transform.o build/Genomic_Data.o build/Splice_Sites.o build/Supporting_Methods.o build/Test.o build/UTRs.o build/main.o -Finished building target: utrrnaseq - -make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/utrrnaseq' -cd bam2wig; make; -make[4]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2wig' -make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. -make[4]: Nothing to be done for 'all'. -make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2wig' -make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs' -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o gene.o gene.cc In file included from /usr/include/c++/12/vector:70, from ../include/types.hh:36: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': @@ -1852,6 +1860,12 @@ 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o evaluation.o evaluation.cc +In file included from /usr/include/c++/12/vector:70, + from src/Genomic_Data.hpp:9: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from ../include/types.hh:38, @@ -1876,7 +1890,36 @@ /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void boost::assign_detail::call_push_back::operator()(T&&) [with T = double; C = std::vector >]' at /usr/include/boost/assign/list_inserter.hpp:91:25, + inlined from 'void boost::assign::list_inserter::insert(single_arg_type, T&&) [with T = double; Function = boost::assign_detail::call_push_back > >; Argument = double]' at /usr/include/boost/assign/list_inserter.hpp:414:20, + inlined from 'boost::assign::list_inserter& boost::assign::list_inserter::operator()(Ts&& ...) [with Ts = {double}; Function = boost::assign_detail::call_push_back > >; Argument = double]' at /usr/include/boost/assign/list_inserter.hpp:406:19, + inlined from 'boost::assign::list_inserter >, V> boost::assign::operator+=(std::vector<_Tp, _Alloc>&, V2&&) [with V = double; A = std::allocator; V2 = double]' at /usr/include/boost/assign/std/vector.hpp:42:30, + inlined from 'static void UTRs::compute_UTRs(const Genomic_Data::Scaff_plus_Gen_Data&, const std::map&)' at src/UTRs.cpp:382:7: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.cc +Finished building: src/UTRs.cpp + +Building file: src/main.cpp +Invoking: GCC C++ Compiler: g++ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/main.d" -MT"build/main.o" -o "build/main.o" "src/main.cpp" +Finished building: src/main.cpp + +Building target: utrrnaseq +Invoking: GCC C++ Linker +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o utrrnaseq build/Compute_UTRs.o build/Coord_Transform.o build/Genomic_Data.o build/Splice_Sites.o build/Supporting_Methods.o build/Test.o build/UTRs.o build/main.o +Finished building target: utrrnaseq + +make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/utrrnaseq' +cd bam2wig; make; +make[4]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2wig' +make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +make[4]: Nothing to be done for 'all'. +make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2wig' +make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneticcode.o geneticcode.cc In file included from /usr/include/c++/12/list:64, from ../include/vitmatrix.hh:17, @@ -1893,13 +1936,13 @@ /usr/include/c++/12/bits/list.tcc:286:29: note: parameter passing for argument of type 'std::_List_const_iterator' changed in GCC 7.1 286 | _M_assign_dispatch(__x.begin(), __x.end(), __false_type()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc In member function 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = PP::Match; _Alloc = std::allocator]', inlined from 'std::__cxx11::list<_Tp, _Alloc>& std::__cxx11::list<_Tp, _Alloc>::operator=(const std::__cxx11::list<_Tp, _Alloc>&) [with _Tp = PP::Match; _Alloc = std::allocator]' at /usr/include/c++/12/bits/list.tcc:267:5, inlined from 'Gene::Gene(const Gene&)' at gene.cc:1391:28: /usr/include/c++/12/bits/list.tcc:286:29: note: parameter passing for argument of type 'std::_List_const_iterator' changed in GCC 7.1 286 | _M_assign_dispatch(__x.begin(), __x.end(), __false_type()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc In file included from /usr/include/c++/12/vector:70, from ../include/matrix.hh:12, from ../include/motif.hh:12, @@ -1915,6 +1958,7 @@ 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc In file included from /usr/include/c++/12/vector:70, from ../include/matrix.hh:12, from ../include/motif.hh:12: @@ -1948,9 +1992,9 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc In file included from /usr/include/c++/12/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, @@ -1998,6 +2042,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc In file included from /usr/include/c++/12/map:60, from ../include/types.hh:39, from ../include/hints.hh:12, @@ -2016,8 +2063,6 @@ /usr/include/c++/12/bits/stl_algo.h:5334:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:5334:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:5334:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc In function '_OIter std::set_difference(_IIter1, _IIter1, _IIter2, _IIter2, _OIter) [with _IIter1 = _Rb_tree_const_iterator; _IIter2 = _Rb_tree_const_iterator; _OIter = insert_iterator >]', inlined from 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)' at extrinsicinfo.cc:2518:20: /usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 @@ -2102,17 +2147,6 @@ | ^ /usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:5399:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator' changed in GCC 7.1 -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc -In file included from /usr/include/c++/12/bits/stl_algo.h:60, - from /usr/include/c++/12/algorithm:61, - from ../include/types.hh:38, - from ../include/merkmal.hh:14, - from merkmal.cc:10: -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from ../include/types.hh:36, from ../include/vitmatrix.hh:12, @@ -2121,8 +2155,6 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/map:60, from ../include/types.hh:39: /usr/include/c++/12/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(const_iterator, const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': @@ -2144,38 +2176,16 @@ /usr/include/c++/12/bits/stl_tree.h:1238:21: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 1238 | _M_erase_aux(__first, __last); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::size_type std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const _Key&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::map<_Key, _Tp, _Compare, _Alloc>::size_type std::map<_Key, _Tp, _Compare, _Alloc>::erase(const key_type&) [with _Key = SubstateId; _Tp = ViterbiSubmapEntry; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_map.h:1117:26, inlined from 'int ViterbiSubmapType::eraseUnneededSubstate(SubstateId)' at vitmatrix.cc:103:18: /usr/include/c++/12/bits/stl_tree.h:2520:19: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2520 | _M_erase_aux(__p.first, __p.second); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/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_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {ViterbiEntryType}; _Tp = ViterbiEntryType; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1802 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {ViterbiEntryType}; _Tp = ViterbiEntryType; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = ViterbiEntryType; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void ViterbiColumnType::addState(int, signed char)' at vitmatrix.cc:289:14: @@ -2206,14 +2216,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 926 | std::forward<_Pair>(__x)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/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_less_iter]': -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1908 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: @@ -2239,6 +2241,49 @@ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o lldouble.o lldouble.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc +In file included from /usr/include/c++/12/bits/stl_algo.h:60, + from /usr/include/c++/12/algorithm:61, + from ../include/types.hh:38, + from ../include/merkmal.hh:14, + from merkmal.cc:10: +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/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_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1802 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/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_less_iter]': +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1908 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'static std::vector CRF::capOutliers(std::vector)' at merkmal.cc:841:11: @@ -2293,15 +2338,12 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void CRF::onlineLargeMarginTraining(Parameters*, std::vector, FeatureCollection&)' at merkmal.cc:396:14: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc In file included from /usr/include/c++/12/vector:70, from ../include/matrix.hh:12, from ../include/motif.hh:12, @@ -2318,12 +2360,15 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o fasta.o fasta.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o ncmodel.o ncmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o parser/parse.o parser/parse.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc In file included from /usr/include/c++/12/vector:70, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, @@ -2333,14 +2378,13 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.cc In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'void NcModel::computeLengthDistributions()' at ncmodel.cc:142:25: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc In file included from /usr/include/c++/12/vector:70, from ../include/matrix.hh:12, from ../include/motif.hh:12, @@ -2357,7 +2401,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from ../include/types.hh:38, @@ -2415,6 +2458,7 @@ 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc In file included from /usr/include/c++/12/vector:70, from ../include/types.hh:36, from ../include/geneticcode.hh:12, @@ -2423,17 +2467,6 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void GeneMSA::calcConsScore(std::__cxx11::list&, const std::vector&, std::string)' at geneMSA.cc:1705:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc In file included from /usr/include/c++/12/vector:70, from ../include/matrix.hh:12, from ../include/contTimeMC.hh:13, @@ -2489,7 +2522,36 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void GeneMSA::calcConsScore(std::__cxx11::list&, const std::vector&, std::string)' at geneMSA.cc:1705:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc +In file included from /usr/include/c++/12/vector:70, + from ../include/types.hh:36, + from ../include/hints.hh:12, + from ../include/extrinsicinfo.hh:15, + from ../include/compgenepred.hh:12, + from compgenepred.cc:8: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'AugustusGraph::AugustusGraph(std::__cxx11::list*, const char*)' at ../include/graph.hh:344:25: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void cumValues::addLogliks(std::vector*)' at ../include/geneMSA.hh:41:21, inlined from 'void GeneMSA::computeOmegasEff(std::__cxx11::list&, const std::vector&, PhyloTree*, std::ofstream*)' at geneMSA.cc:1560:17: @@ -2509,7 +2571,6 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Treenode::resizeTable(int, double)' at phylotree.cc:55:17, inlined from 'double PhyloTree::pruningAlgor(std::vector&, Evo*, int)' at phylotree.cc:249:23: @@ -2562,46 +2623,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc -In file included from /usr/include/c++/12/vector:70, - from ../include/types.hh:36, - from ../include/hints.hh:12, - from ../include/extrinsicinfo.hh:15, - from ../include/compgenepred.hh:12, - from compgenepred.cc:8: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'AugustusGraph::AugustusGraph(std::__cxx11::list*, const char*)' at ../include/graph.hh:344:25: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from ../include/types.hh:36, - from ../include/exoncand.hh:13, - from ../include/orthoexon.hh:11, - from orthoexon.cc:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void OrthoExon::setOmega(std::vector*, CodonEvo*, bool)' at orthoexon.cc:168:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'OrthoExon::OrthoExon(int_fast64_t, size_t)' at orthoexon.cc:21:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void CompGenePred::runPredictionOrTest()' at compgenepred.cc:282:23: @@ -2626,8 +2647,30 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.cc +In file included from /usr/include/c++/12/vector:70, + from ../include/types.hh:36, + from ../include/exoncand.hh:13, + from ../include/orthoexon.hh:11, + from orthoexon.cc:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void OrthoExon::setOmega(std::vector*, CodonEvo*, bool)' at orthoexon.cc:168:25: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'OrthoExon::OrthoExon(int_fast64_t, size_t)' at orthoexon.cc:21:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o train_logReg_param.o train_logReg_param.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o tokenizer.o tokenizer.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o sqliteDB.o sqliteDB.cc @@ -2636,6 +2679,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o introntrain.o introntrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exontrain.o exontrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrtrain.o utrtrain.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o dummy.o dummy.cc In file included from /usr/include/c++/12/vector:70, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, @@ -2667,7 +2711,6 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o dummy.o dummy.cc In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]', inlined from 'void BinnedMMGroup::addProb(Double)' at ../include/merkmal.hh:126:47, @@ -2682,11 +2725,15 @@ 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc -cp -f prepareAlign ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 +cp -f prepareAlign ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 +cp -f load2sqlitedb ../bin/ +echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 In file included from /usr/include/c++/12/vector:70, from ../include/types.hh:36, from ../include/properties.hh:14, @@ -2703,14 +2750,10 @@ 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cp -f load2db ../bin/ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 -cp -f pp_simScore ../bin/ -echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 -cp -f getSeq ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 -cp -f load2sqlitedb ../bin/ +cp -f getSeq ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 +cp -f pp_simScore ../bin/ In file included from /usr/include/c++/12/vector:70, from ../include/types.hh:36, from etraining.cc:9: @@ -2732,13 +2775,13 @@ asciidoctor -a docdate='' -b manpage --destination-dir=debian/mansrc/ mansrc/*adoc make[1]: Leaving directory '/build/augustus-3.5.0+dfsg' dh_auto_test - make -j3 test + make -j4 test make[1]: Entering directory '/build/augustus-3.5.0+dfsg' mkdir -p bin cd src && make mkdir -p bin -make[2]: Entering directory '/build/augustus-3.5.0+dfsg/src' cd auxprogs && make +make[2]: Entering directory '/build/augustus-3.5.0+dfsg/src' make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs' cd aln2wig; make; make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/aln2wig' @@ -2760,8 +2803,8 @@ make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src;make) make[4]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam/src' -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/src' mkdir -p ../../../bin mv filterBam ../../../bin/filterBam @@ -2803,7 +2846,7 @@ test_cgp_sqlite_hints (examples.test_examples.TestExamples.test_cgp_sqlite_hints) ... ok ---------------------------------------------------------------------- -Ran 8 tests in 1549.775s +Ran 8 tests in 1636.311s OK Removing generated test files... @@ -2816,7 +2859,7 @@ test_bam2hints_pipes (auxprogs.bam2hints.test_bam2hints.TestBam2Hints.test_bam2hints_pipes) ... ok ---------------------------------------------------------------------- -Ran 2 tests in 0.028s +Ran 2 tests in 0.026s OK cd tests/short && ./execute_test.py --html bam2wig @@ -2824,7 +2867,7 @@ test_bam2wig_region (auxprogs.bam2wig.test_bam2wig.TestBam2Wig.test_bam2wig_region) ... ok ---------------------------------------------------------------------- -Ran 2 tests in 0.050s +Ran 2 tests in 0.056s OK cd tests/short && ./execute_test.py --html filterbam @@ -2855,7 +2898,7 @@ test_calmd_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_paired_pairwiseAlignments) ... ok ---------------------------------------------------------------------- -Ran 25 tests in 1.950s +Ran 25 tests in 1.235s OK make[1]: Leaving directory '/build/augustus-3.5.0+dfsg' @@ -2922,28 +2965,28 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2db contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/pp_simScore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2sqlitedb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/augustus/usr/bin/filterBam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/augustus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/augustus/usr/bin/getSeq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/augustus/usr/bin/joingenes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/augustus/usr/bin/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/homGeneMapping contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/augustus/usr/bin/etraining contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/augustus/usr/bin/filterBam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2sqlitedb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/augustus/usr/bin/getSeq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/prepareAlign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2db contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/augustus/usr/bin/etraining contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/fastBlockSearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/augustus/usr/bin/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/augustus/usr/bin/joingenes 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: package augustus: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'augustus-data' in '../augustus-data_3.5.0+dfsg-2_all.deb'. -dpkg-deb: building package 'augustus' in '../augustus_3.5.0+dfsg-2_armhf.deb'. dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.5.0+dfsg-2_armhf.deb'. +dpkg-deb: building package 'augustus-data' in '../augustus-data_3.5.0+dfsg-2_all.deb'. dpkg-deb: building package 'augustus-doc' in '../augustus-doc_3.5.0+dfsg-2_all.deb'. +dpkg-deb: building package 'augustus' in '../augustus_3.5.0+dfsg-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../augustus_3.5.0+dfsg-2_armhf.buildinfo dpkg-genchanges --build=binary -O../augustus_3.5.0+dfsg-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2951,12 +2994,14 @@ 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/10065/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/10065/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/3382 and its subdirectories -I: Current time: Fri May 26 04:42:28 -12 2023 -I: pbuilder-time-stamp: 1685119348 +I: removing directory /srv/workspace/pbuilder/10065 and its subdirectories +I: Current time: Sat May 27 07:40:16 +14 2023 +I: pbuilder-time-stamp: 1685122816