Diff of the two buildlogs: -- --- b1/build.log 2023-05-09 18:38:32.904351367 +0000 +++ b2/build.log 2023-05-09 18:47:46.404138459 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 9 06:13:09 -12 2023 -I: pbuilder-time-stamp: 1683655989 +I: Current time: Wed May 10 08:39:01 +14 2023 +I: pbuilder-time-stamp: 1683657541 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 [./last-align_1447.orig.tar.xz] I: copying [./last-align_1447-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Feb 5 08:29:38 2023 -12 +gpgv: Signature made Mon Feb 6 10:29:38 2023 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,135 +30,167 @@ dpkg-source: info: applying fix-shebang.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/23189/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/22546/tmp/hooks/D01_modify_environment starting +debug: Running on virt64a. +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 10 08:39 /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/22546/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/22546/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='7d7632083844426196f55f2abe4d89d4' - 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='23189' - PS1='# ' - PS2='> ' + INVOCATION_ID=2e5e956972ec4c58b6f32f5a9f1160d5 + 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=22546 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.W1slieVJ/pbuilderrc_hEDq --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.W1slieVJ/b1 --logfile b1/build.log last-align_1447-1.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.W1slieVJ/pbuilderrc_XSK9 --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.W1slieVJ/b2 --logfile b2/build.log --extrapackages usrmerge last-align_1447-1.dsc' + SUDO_GID=114 + SUDO_UID=108 + 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 wbq0 5.10.0-22-armmp #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 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/23189/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 10 08:39 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/22546/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -275,7 +307,7 @@ Get: 69 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf python3-pil armhf 9.4.0-1.1+b1 [438 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] -Fetched 31.0 MB in 6s (5083 kB/s) +Fetched 31.0 MB in 3s (11.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19329 files and directories currently installed.) @@ -576,8 +608,19 @@ 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/last-align-1447/ && 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 > ../last-align_1447-1_source.changes +I: user script /srv/workspace/pbuilder/22546/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/22546/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/last-align-1447/ && 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 > ../last-align_1447-1_source.changes dpkg-buildpackage: info: source package last-align dpkg-buildpackage: info: source version 1447-1 dpkg-buildpackage: info: source distribution unstable @@ -587,14 +630,14 @@ debian/rules clean dh clean debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/last-align-1447' +make[1]: ingresso nella directory «/build/last-align-1447» dh_auto_clean - make -j3 clean -make[2]: Entering directory '/build/last-align-1447' -make[3]: Entering directory '/build/last-align-1447/src' + make -j4 clean +make[2]: ingresso nella directory «/build/last-align-1447» +make[3]: ingresso nella directory «/build/last-align-1447/src» rm -f ../bin/lastdb ../bin/lastal ../bin/last-split ../bin/lastdb5 ../bin/lastal5 ../bin/last-split5 ../bin/last-merge-batches ../bin/last-pair-probs ../bin/lastdb8 ../bin/lastal8 ../bin/last-split8 *.o* */*.o* -make[3]: Leaving directory '/build/last-align-1447/src' -make[2]: Leaving directory '/build/last-align-1447' +make[3]: uscita dalla directory «/build/last-align-1447/src» +make[2]: uscita dalla directory «/build/last-align-1447» for i in last-merge-batches last-pair-probs last-split last-split5 lastal lastal5 lastdb lastdb5; \ do \ for j in avx avx2 sse2 sse3 sse4.1 ssse3 sse3 sse2 sse ; \ @@ -602,7 +645,7 @@ rm -f bin/$i-$j ; \ done ; \ done -make[1]: Leaving directory '/build/last-align-1447' +make[1]: uscita dalla directory «/build/last-align-1447» dh_clean debian/rules binary dh binary @@ -610,11 +653,11 @@ dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build -make[1]: Entering directory '/build/last-align-1447' +make[1]: ingresso nella directory «/build/last-align-1447» dh_auto_build - make -j3 "INSTALL=install --strip-program=true" -make[2]: Entering directory '/build/last-align-1447' -make[3]: Entering directory '/build/last-align-1447/src' + make -j4 "INSTALL=install --strip-program=true" +make[2]: ingresso nella directory «/build/last-align-1447» +make[3]: ingresso nella directory «/build/last-align-1447/src» g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o Alphabet.o Alphabet.cc ../build/seed-inc.sh ../data/*.seed > CyclicSubsetSeedData.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o LambdaCalculator.o LambdaCalculator.cc @@ -628,6 +671,7 @@ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o tantan.o tantan.cc echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o MultiSequence.o MultiSequence.cc +g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc In file included from /usr/include/c++/12/vector:70, from mcf_substitution_matrix_stats.hh:23, from mcf_substitution_matrix_stats.cc:4: @@ -646,7 +690,6 @@ /usr/include/c++/12/bits/stl_vector.h:1435:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1435 | _M_fill_insert(begin() + __offset, __n, __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o lastdb.o lastdb.cc @@ -667,6 +710,9 @@ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc +g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/last_split_options.o split/last_split_options.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp In file included from /usr/include/c++/12/vector:70, from mcf_gap_costs.hh:20, from mcf_frameshift_xdrop_aligner.hh:21, @@ -691,10 +737,8 @@ /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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/last_split_options.o split/last_split_options.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp In file included from /usr/include/c++/12/vector:70, from alp/sls_pvalues.hpp:41, from alp/sls_alignment_evaluer.hpp:39, @@ -781,8 +825,6 @@ /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 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from alp/sls_alp_regression.hpp:46, @@ -819,6 +861,8 @@ 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*, std::vector > >’ changed in GCC 7.1 +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_alp.o alp/sls_alp.cpp 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 double Sls::alp_reg::median(long int, double*)’ at alp/sls_alp_regression.cpp:643:6: @@ -879,6 +923,8 @@ /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 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_basic.o alp/sls_basic.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from alp/sls_alp_regression.hpp:46, @@ -901,7 +947,6 @@ /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 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_alp.o alp/sls_alp.cpp 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 ‘Sls::importance_sampling::importance_sampling(Sls::alp_data*, long int, long int, double, long int, long int**, double*, double*)’ at alp/sls_alp_data.cpp:1269:8: @@ -922,8 +967,6 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_basic.o alp/sls_basic.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp @@ -934,6 +977,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp In file included from /usr/include/c++/12/vector:70, from alp/sls_fsa1_pvalues.hpp:41, from alp/sls_falp_alignment_evaluer.hpp:40, @@ -1020,27 +1064,8 @@ /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 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp -In file included from /usr/include/c++/12/vector:70, - from alp/sls_fsa1_utils.hpp:40, - from alp/sls_fsa1_utils.cpp:36: -/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 ‘static void Sls::FSA_utils::multiply_matrix_and_vector(const std::vector >&, const std::vector&, std::vector&)’ at alp/sls_fsa1_utils.cpp:1805:13: -/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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o Alignment.o Alignment.cc -In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, - inlined from ‘static void Sls::FSA_utils::multiply_matrices(const std::vector >&, const std::vector >&, std::vector >&)’ at alp/sls_fsa1_utils.cpp:1758:17: -/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 file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from alp/sls_alp_regression.hpp:46, @@ -1063,6 +1088,24 @@ /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 file included from /usr/include/c++/12/vector:70, + from alp/sls_fsa1_utils.hpp:40, + from alp/sls_fsa1_utils.cpp:36: +/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 ‘static void Sls::FSA_utils::multiply_matrix_and_vector(const std::vector >&, const std::vector&, std::vector&)’ at alp/sls_fsa1_utils.cpp:1805:13: +/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 ‘static void Sls::FSA_utils::multiply_matrices(const std::vector >&, const std::vector >&, std::vector >&)’ at alp/sls_fsa1_utils.cpp:1758:17: +/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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o AlignmentPot.o AlignmentPot.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, @@ -1196,6 +1239,7 @@ g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o lastal.o lastal.cc g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc +g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.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 Sls::IS1_general_simulation::calculate_weight_W1_for_fixed_lengths_using_recursions(long int, long int, double&, bool, std::vector >*, std::vector >*)’ at alp/sls_fsa1.cpp:2237:23: @@ -1207,6 +1251,45 @@ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from split/cbrc_unsplit_alignment.hh:13, + from split/cbrc_split_aligner.hh:7, + from split/cbrc_split_aligner.cc:4: +/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 ‘std::vector cbrc::SplitAligner::marginalProbs(unsigned int, unsigned int, unsigned int, unsigned int) const’ at split/cbrc_split_aligner.cc:750:23: +/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); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, + inlined from ‘std::vector cbrc::SplitAligner::marginalProbs(unsigned int, unsigned int, unsigned int, unsigned int) const’ at split/cbrc_split_aligner.cc:754:23: +/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); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/algorithm:61, + from Mmap.hh:12, + from VectorOrMmap.hh:8, + from MultiSequence.hh:14, + from last.hh:8, + from lastal.cc:5: +/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 file included from /usr/include/c++/12/bits/stl_algo.h:60: +/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 = cbrc::AlignmentText; _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 member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘static void Sls::test::collect_and_output_E_distr_upto_fixed_ALP(long int, std::string, Sls::two_dim_layer_alignment_algorithm&, Sls::IS1_general_simulation&, long int, double, long int, long int, Sls::FALP_set_of_parameters&, bool, bool, Sls::IS1_general*, double*, long int*)’ at alp/sls_fsa1.cpp:7214:30: /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 @@ -1247,45 +1330,6 @@ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from split/cbrc_unsplit_alignment.hh:13, - from split/cbrc_split_aligner.hh:7, - from split/cbrc_split_aligner.cc:4: -/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 ‘std::vector cbrc::SplitAligner::marginalProbs(unsigned int, unsigned int, unsigned int, unsigned int) const’ at split/cbrc_split_aligner.cc:750:23: -/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); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, - inlined from ‘std::vector cbrc::SplitAligner::marginalProbs(unsigned int, unsigned int, unsigned int, unsigned int) const’ at split/cbrc_split_aligner.cc:754:23: -/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); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/algorithm:61, - from Mmap.hh:12, - from VectorOrMmap.hh:8, - from MultiSequence.hh:14, - from last.hh:8, - from lastal.cc:5: -/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 file included from /usr/include/c++/12/bits/stl_algo.h:60: -/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 = cbrc::AlignmentText; _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_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, @@ -1294,6 +1338,7 @@ /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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/last-split-main.o split/last-split-main.cc In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘static void Sls::test::collect_and_output_E_distr_upto_fixed_ALP_with_saving_of_states(bool, double&, long int, std::string, Sls::two_dim_layer_alignment_algorithm&, Sls::IS1_general_simulation&, long int, double, long int, long int, Sls::FALP_set_of_parameters&, bool&, bool, bool, double, bool&, long int&, double, bool, Sls::mult_states_type*, Sls::mult_states_type*&, long int&, bool, long int, Sls::IS1_general*, double*, long int*, bool)’ at alp/sls_fsa1.cpp:9334:30: /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 @@ -1357,11 +1402,24 @@ /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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc /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_comp_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_comp_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::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_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_comp_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>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘static void Sls::test::collect_and_output_E_distr_upto_fixed_ALP_with_saving_of_states(bool, double&, long int, std::string, Sls::two_dim_layer_alignment_algorithm&, Sls::IS1_general_simulation&, long int, double, long int, long int, Sls::FALP_set_of_parameters&, bool&, bool, bool, double, bool&, long int&, double, bool, Sls::mult_states_type*, Sls::mult_states_type*&, long int&, bool, long int, Sls::IS1_general*, double*, long int*, bool)’ at alp/sls_fsa1.cpp:9334:30: /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 @@ -1372,11 +1430,6 @@ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/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_comp_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>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘static void Sls::test::collect_and_output_E_distr_upto_fixed_ALP_with_saving_of_states(bool, double&, long int, std::string, Sls::two_dim_layer_alignment_algorithm&, Sls::IS1_general_simulation&, long int, double, long int, long int, Sls::FALP_set_of_parameters&, bool&, bool, bool, double, bool&, long int&, double, bool, Sls::mult_states_type*, Sls::mult_states_type*&, long int&, bool, long int, Sls::IS1_general*, double*, long int*, bool)’ at alp/sls_fsa1.cpp:9562:27: /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 @@ -1407,19 +1460,11 @@ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/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_comp_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_comp_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_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = cbrc::Alignment; _Compare = __gnu_cxx::__ops::_Iter_comp_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, | ^~~~~~~~~~~~~ +g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/last-split.o split/last-split.cc /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, @@ -1439,6 +1484,7 @@ /usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1629 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o MultiSequence.o5 MultiSequence.cc In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const cbrc::Alignment&, const cbrc::Alignment&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘void cbrc::AlignmentPot::sort()’ at AlignmentPot.hh:28:26, @@ -1517,7 +1563,6 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/last-split-main.o split/last-split-main.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 ‘void alignOneQuery(LastAligner&, cbrc::MultiSequence&, size_t, size_t, size_t, bool)’ at lastal.cc:1197:11, @@ -1565,18 +1610,18 @@ /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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/last-split.o split/last-split.cc -g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o MultiSequence.o5 MultiSequence.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o MultiSequenceQual.o5 MultiSequenceQual.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SubsetSuffixArray.o5 SubsetSuffixArray.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SubsetSuffixArraySort.o5 SubsetSuffixArraySort.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o lastdb.o5 lastdb.cc +g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o Alignment.o5 Alignment.cc In file included from lastdb.cc:6: last.hh:21:36: warning: right shift count >= width of type [-Wshift-count-overflow] 21 | const size_t posLimit = size_t(-1) >> ((sizeof(size_t) - posSize) * CHAR_BIT); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o Alignment.o5 Alignment.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o AlignmentPot.o5 AlignmentPot.cc +g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o AlignmentWrite.o5 AlignmentWrite.cc +g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o Centroid.o5 Centroid.cc In file included from /usr/include/c++/12/algorithm:61, from Centroid.hh:15, from Alignment.hh:8, @@ -1655,20 +1700,20 @@ /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++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o AlignmentWrite.o5 AlignmentWrite.cc -g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o Centroid.o5 Centroid.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o DiagonalTable.o5 DiagonalTable.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SegmentPair.o5 SegmentPair.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SegmentPairPot.o5 SegmentPairPot.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SubsetSuffixArraySearch.o5 SubsetSuffixArraySearch.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o lastal.o5 lastal.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/cbrc_split_aligner.o5 split/cbrc_split_aligner.cc +g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/mcf_last_splitter.o5 split/mcf_last_splitter.cc In file included from lastal.cc:5: last.hh:21:36: warning: right shift count >= width of type [-Wshift-count-overflow] 21 | const size_t posLimit = size_t(-1) >> ((sizeof(size_t) - posSize) * CHAR_BIT); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/mcf_last_splitter.o5 split/mcf_last_splitter.cc g++ -DLAST_POS_BYTES=5 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/last-split.o5 split/last-split.cc +cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-1447=. -fstack-protector-strong -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c +g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o last-pair-probs.o last-pair-probs.cc In file included from /usr/include/c++/12/vector:70, from split/cbrc_unsplit_alignment.hh:13, from split/cbrc_split_aligner.hh:7, @@ -1689,81 +1734,6 @@ 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/algorithm:61, - from Mmap.hh:12, - from VectorOrMmap.hh:8, - from MultiSequence.hh:14, - from last.hh:8: -/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 file included from /usr/include/c++/12/bits/stl_algo.h:60: -/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 = cbrc::AlignmentText; _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_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); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from CyclicSubsetSeed.hh:41, - from last.hh:7: -/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const cbrc::Alignment&}; _Tp = cbrc::Alignment; _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>:: - | ^~~~~~~~~~~~~~~~~~~ -cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -ffile-prefix-map=/build/last-align-1447=. -fstack-protector-strong -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c -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 = cbrc::Alignment; _Alloc = std::allocator]’, - inlined from ‘void cbrc::AlignmentPot::add(const cbrc::Alignment&)’ at AlignmentPot.hh:18:53, - inlined from ‘void alignGapped(LastAligner&, cbrc::AlignmentPot&, cbrc::SegmentPairPot&, const SeqData&, const SubstitutionMatrices&, Phase::Enum)’ at lastal.cc:802:47: -/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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o last-pair-probs.o last-pair-probs.cc -/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const cbrc::AlignmentText&}; _Tp = cbrc::AlignmentText; _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>::push_back(const value_type&) [with _Tp = cbrc::AlignmentText; _Alloc = std::allocator]’, - inlined from ‘void writeAlignment(LastAligner&, const cbrc::MultiSequence&, const SeqData&, const cbrc::Alignment&, const cbrc::AlignmentExtras&)’ at lastal.cc:589:31: -/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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc -/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_comp_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_comp_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::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_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_comp_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_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = cbrc::Alignment; _Compare = __gnu_cxx::__ops::_Iter_comp_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/algorithm:61, from last-pair-probs.cc:9: /usr/include/c++/12/bits/stl_algo.h: In function ‘_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Alignment*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 @@ -1774,30 +1744,25 @@ /usr/include/c++/12/bits/stl_algo.h:2615:5: 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 ‘_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Alignment*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:2615:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 -/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: -/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, - | ^~~~~~~~~~~ -/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 +In file included from /usr/include/c++/12/algorithm:61, + from Mmap.hh:12, + from VectorOrMmap.hh:8, + from MultiSequence.hh:14, + from last.hh:8: +/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_comp_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: 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: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); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, - inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1900:25, - inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27: -/usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1629 | std::__make_heap(__first, __middle, __comp); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Alignment*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:2682:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2682 | __merge_sort_with_buffer(_RandomAccessIterator __first, @@ -1846,6 +1811,11 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2659 | __first + __step_size, __last, __result, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_algo.h:60: +/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 = cbrc::AlignmentText; _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_algo.h: In function ‘_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/12/bits/stl_algo.h:1281:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1281 | __rotate(_RandomAccessIterator __first, @@ -1882,28 +1852,6 @@ | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:2390:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:2390:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 -In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, - inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const cbrc::Alignment&, const cbrc::Alignment&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, - inlined from ‘void cbrc::AlignmentPot::sort()’ at AlignmentPot.hh:28:26, - inlined from ‘void scan(LastAligner&, const cbrc::MultiSequence&, const SeqData&, const SubstitutionMatrices&)’ at lastal.cc:1048:47: -/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1937 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1938 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1939 | __comp); - | ~~~~~~~ -In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, - inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, - inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const cbrc::Alignment&, const cbrc::Alignment&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, - inlined from ‘void cbrc::AlignmentPot::sort()’ at AlignmentPot.hh:28:26, - inlined from ‘void scan(LastAligner&, const cbrc::MultiSequence&, const SeqData&, const SubstitutionMatrices&)’ at lastal.cc:1048:47: -/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘_FIter std::_V2::rotate(_FIter, _FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator >]’, inlined from ‘_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Alignment*; _Distance = int]’ at /usr/include/c++/12/bits/stl_algo.h:2383:20, inlined from ‘void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Alignment*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:2435:30: @@ -1959,7 +1907,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~ 2733 | __comp); | ~~~~~~~ -g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__inplace_stable_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:2739:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2739 | __inplace_stable_sort(_RandomAccessIterator __first, @@ -2282,6 +2229,140 @@ | ~~~~~~~~~~~~~~~~~~ 2753 | __comp); | ~~~~~~~ +/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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc +In file included from /usr/include/c++/12/vector:70, + from last-pair-probs.hh:28, + from last-pair-probs.cc:4: +/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Alignment}; _Tp = Alignment; _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 = {Alignment}; _Tp = Alignment; _Alloc = std::allocator]’, + inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Alignment; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from ‘bool readBatch(std::istream&, char, double, const std::set >&, std::vector&, std::vector&, std::vector&)’ at last-pair-probs.cc:492:21: +/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>::emplace_back(_Args&& ...) [with _Args = {Alignment}; _Tp = Alignment; _Alloc = std::allocator]’, + inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Alignment; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from ‘bool readBatch(std::istream&, char, double, const std::set >&, std::vector&, std::vector&, std::vector&)’ at last-pair-probs.cc:495:16: +/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>::emplace_back(_Args&& ...) [with _Args = {Alignment}; _Tp = Alignment; _Alloc = std::allocator]’, + inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Alignment; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from ‘bool readBatch(std::istream&, char, double, const std::set >&, std::vector&, std::vector&, std::vector&)’ at last-pair-probs.cc:501:19: +/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 function ‘void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, + inlined from ‘void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:5034:36, + inlined from ‘bool readBatch(std::istream&, char, double, const std::set >&, std::vector&, std::vector&, std::vector&)’ at last-pair-probs.cc:509:14: +/usr/include/c++/12/bits/stl_algo.h:5001:36: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 5001 | std::__stable_sort_adaptive(__first, __last, __buf.begin(), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 5002 | _DistanceType(__buf.size()), __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:4999:35: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 4999 | std::__inplace_stable_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from CyclicSubsetSeed.hh:41, + from last.hh:7: +/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const cbrc::Alignment&}; _Tp = cbrc::Alignment; _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 = cbrc::Alignment; _Alloc = std::allocator]’, + inlined from ‘void cbrc::AlignmentPot::add(const cbrc::Alignment&)’ at AlignmentPot.hh:18:53, + inlined from ‘void alignGapped(LastAligner&, cbrc::AlignmentPot&, cbrc::SegmentPairPot&, const SeqData&, const SubstitutionMatrices&, Phase::Enum)’ at lastal.cc:802:47: +/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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc +g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o ScoreMatrix.o ScoreMatrix.cc +/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const cbrc::AlignmentText&}; _Tp = cbrc::AlignmentText; _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>::push_back(const value_type&) [with _Tp = cbrc::AlignmentText; _Alloc = std::allocator]’, + inlined from ‘void writeAlignment(LastAligner&, const cbrc::MultiSequence&, const SeqData&, const cbrc::Alignment&, const cbrc::AlignmentExtras&)’ at lastal.cc:589:31: +/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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o LastdbArguments.o LastdbArguments.cc +/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_comp_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_comp_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::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_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_comp_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_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = cbrc::Alignment; _Compare = __gnu_cxx::__ops::_Iter_comp_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::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: +/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, + | ^~~~~~~~~~~ +/usr/include/c++/12/bits/stl_heap.h:340:5: 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_comp_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); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, + inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1900:25, + inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27: +/usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1629 | std::__make_heap(__first, __middle, __comp); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, + inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const cbrc::Alignment&, const cbrc::Alignment&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, + inlined from ‘void cbrc::AlignmentPot::sort()’ at AlignmentPot.hh:28:26, + inlined from ‘void scan(LastAligner&, const cbrc::MultiSequence&, const SeqData&, const SubstitutionMatrices&)’ at lastal.cc:1048:47: +/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1937 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1938 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1939 | __comp); + | ~~~~~~~ +In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, + inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, + inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const cbrc::Alignment&, const cbrc::Alignment&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, + inlined from ‘void cbrc::AlignmentPot::sort()’ at AlignmentPot.hh:28:26, + inlined from ‘void scan(LastAligner&, const cbrc::MultiSequence&, const SeqData&, const SubstitutionMatrices&)’ at lastal.cc:1048:47: +/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /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 = cbrc::AlignmentText; _Compare = __gnu_cxx::__ops::_Iter_comp_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, @@ -2338,6 +2419,24 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from ScoreMatrix.hh:18, + from ScoreMatrix.cc:3: +/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 ‘std::istream& cbrc::operator>>(std::istream&, ScoreMatrix&)’ at ScoreMatrix.cc:271:25: +/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); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, + inlined from ‘std::istream& cbrc::operator>>(std::istream&, ScoreMatrix&)’ at ScoreMatrix.cc:279:25: +/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); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 ‘void alignOneQuery(LastAligner&, cbrc::MultiSequence&, size_t, size_t, size_t, bool)’ at lastal.cc:1197:11, @@ -2380,62 +2479,6 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from last-pair-probs.hh:28, - from last-pair-probs.cc:4: -/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Alignment}; _Tp = Alignment; _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 = {Alignment}; _Tp = Alignment; _Alloc = std::allocator]’, - inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Alignment; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from ‘bool readBatch(std::istream&, char, double, const std::set >&, std::vector&, std::vector&, std::vector&)’ at last-pair-probs.cc:492:21: -/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>::emplace_back(_Args&& ...) [with _Args = {Alignment}; _Tp = Alignment; _Alloc = std::allocator]’, - inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Alignment; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from ‘bool readBatch(std::istream&, char, double, const std::set >&, std::vector&, std::vector&, std::vector&)’ at last-pair-probs.cc:495:16: -/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>::emplace_back(_Args&& ...) [with _Args = {Alignment}; _Tp = Alignment; _Alloc = std::allocator]’, - inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Alignment; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from ‘bool readBatch(std::istream&, char, double, const std::set >&, std::vector&, std::vector&, std::vector&)’ at last-pair-probs.cc:501:19: -/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 function ‘void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, - inlined from ‘void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:5034:36, - inlined from ‘bool readBatch(std::istream&, char, double, const std::set >&, std::vector&, std::vector&, std::vector&)’ at last-pair-probs.cc:509:14: -/usr/include/c++/12/bits/stl_algo.h:5001:36: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 5001 | std::__stable_sort_adaptive(__first, __last, __buf.begin(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 5002 | _DistanceType(__buf.size()), __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:4999:35: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 4999 | std::__inplace_stable_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o ScoreMatrix.o ScoreMatrix.cc -g++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o LastdbArguments.o LastdbArguments.cc -In file included from /usr/include/c++/12/vector:70, - from ScoreMatrix.hh:18, - from ScoreMatrix.cc:3: -/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 ‘std::istream& cbrc::operator>>(std::istream&, ScoreMatrix&)’ at ScoreMatrix.cc:271:25: -/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); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, - inlined from ‘std::istream& cbrc::operator>>(std::istream&, ScoreMatrix&)’ at ScoreMatrix.cc:279:25: -/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++ -DLAST_POS_BYTES=4 -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GeneticCode.o GeneticCode.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split5 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o MultiSequence.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 split/last-split.o5 @@ -2445,28 +2488,28 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastdb5 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o5 MultiSequenceQual.o5 SubsetSuffixArray.o5 SubsetSuffixArraySort.o5 lastdb.o5 -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o split/cbrc_split_aligner.o split/mcf_last_splitter.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/lastal5 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_aligment_path_adder.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o5 AlignmentPot.o5 AlignmentWrite.o5 Centroid.o5 DiagonalTable.o5 MultiSequence.o5 MultiSequenceQual.o5 SegmentPair.o5 SegmentPairPot.o5 SubsetSuffixArray.o5 SubsetSuffixArraySearch.o5 lastal.o5 split/cbrc_split_aligner.o5 split/mcf_last_splitter.o5 -lz -make[3]: Leaving directory '/build/last-align-1447/src' -make[2]: Leaving directory '/build/last-align-1447' -make[1]: Leaving directory '/build/last-align-1447' +make[3]: uscita dalla directory «/build/last-align-1447/src» +make[2]: uscita dalla directory «/build/last-align-1447» +make[1]: uscita dalla directory «/build/last-align-1447» dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install -make[1]: Entering directory '/build/last-align-1447' +make[1]: ingresso nella directory «/build/last-align-1447» /usr/bin/make -j install prefix=/build/last-align-1447/debian/last-align/usr -make[2]: Entering directory '/build/last-align-1447' -make[3]: Entering directory '/build/last-align-1447/src' +make[2]: ingresso nella directory «/build/last-align-1447» +make[3]: ingresso nella directory «/build/last-align-1447/src» echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1447) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh -make[3]: Leaving directory '/build/last-align-1447/src' +make[3]: uscita dalla directory «/build/last-align-1447/src» mkdir -p /build/last-align-1447/debian/last-align/usr/bin cp bin/* /build/last-align-1447/debian/last-align/usr/bin -make[2]: Leaving directory '/build/last-align-1447' -make[1]: Leaving directory '/build/last-align-1447' +make[2]: uscita dalla directory «/build/last-align-1447» +make[1]: uscita dalla directory «/build/last-align-1447» dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman -make[1]: Entering directory '/build/last-align-1447' +make[1]: ingresso nella directory «/build/last-align-1447» dh_installman help2man --no-info --version-string="1447" \ --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \ @@ -2540,7 +2583,7 @@ --name="Keep the first of identical sequences" \ --help-option="-h" \ /build/last-align-1447/debian/last-align/usr/bin/fasta-nr > /build/last-align-1447/debian/last-align/usr/share/man/man1/fasta-nr.1 -make[1]: Leaving directory '/build/last-align-1447' +make[1]: uscita dalla directory «/build/last-align-1447» dh_lintian dh_perl dh_link @@ -2552,22 +2595,22 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastdb5 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastdb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-split5 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-pair-probs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-split contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastdb5 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal5 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-pair-probs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-split5 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastdb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb debian/rules override_dh_gencontrol -make[1]: Entering directory '/build/last-align-1447' +make[1]: ingresso nella directory «/build/last-align-1447» dh_gencontrol -- -VBuilt-Using="simde (= 0.7.4~rc2-2), " -make[1]: Leaving directory '/build/last-align-1447' +make[1]: uscita dalla directory «/build/last-align-1447» dh_md5sums dh_builddeb -dpkg-deb: building package 'last-align-dbgsym' in '../last-align-dbgsym_1447-1_armhf.deb'. -dpkg-deb: building package 'last-align' in '../last-align_1447-1_armhf.deb'. +dpkg-deb: generazione del pacchetto "last-align-dbgsym" in "../last-align-dbgsym_1447-1_armhf.deb". +dpkg-deb: generazione del pacchetto "last-align" in "../last-align_1447-1_armhf.deb". dpkg-genbuildinfo --build=binary -O../last-align_1447-1_armhf.buildinfo dpkg-genchanges --build=binary -O../last-align_1447-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2575,12 +2618,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/22546/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/22546/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/23189 and its subdirectories -I: Current time: Tue May 9 06:38:28 -12 2023 -I: pbuilder-time-stamp: 1683657508 +I: removing directory /srv/workspace/pbuilder/22546 and its subdirectories +I: Current time: Wed May 10 08:47:40 +14 2023 +I: pbuilder-time-stamp: 1683658060