Diff of the two buildlogs: -- --- b1/build.log 2023-05-12 08:35:02.309333185 +0000 +++ b2/build.log 2023-05-12 09:01:38.499417281 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 11 20:12:15 -12 2023 -I: pbuilder-time-stamp: 1683879135 +I: Current time: Fri May 12 22:35:34 +14 2023 +I: pbuilder-time-stamp: 1683880534 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 [./rate4site_3.0.0.orig.tar.gz] I: copying [./rate4site_3.0.0-8.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Jan 19 22:57:32 2022 -12 +gpgv: Signature made Fri Jan 21 00:57:32 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,135 +28,167 @@ dpkg-source: info: applying spelling.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/29878/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3244/tmp/hooks/D01_modify_environment starting +debug: Running on cbxi4b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 12 22:37 /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/3244/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3244/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='84bb9f5a9b6d4d11807d589a619892fd' - 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='29878' - PS1='# ' - PS2='> ' + INVOCATION_ID=e718ee14fb7d4f33bedb12f4ea4bfc43 + 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=3244 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.jXnlD7Vn/pbuilderrc_S1PN --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.jXnlD7Vn/b1 --logfile b1/build.log rate4site_3.0.0-8.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.jXnlD7Vn/pbuilderrc_XmQt --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.jXnlD7Vn/b2 --logfile b2/build.log --extrapackages usrmerge rate4site_3.0.0-8.dsc' + SUDO_GID=116 + SUDO_UID=112 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64a 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-armmp #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/29878/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 12 22:37 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/3244/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -222,7 +254,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] -Fetched 18.0 MB in 1min 1s (297 kB/s) +Fetched 18.0 MB in 2s (7606 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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.) @@ -356,8 +388,19 @@ 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/rate4site-3.0.0/ && 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 > ../rate4site_3.0.0-8_source.changes +I: user script /srv/workspace/pbuilder/3244/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/3244/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/rate4site-3.0.0/ && 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 > ../rate4site_3.0.0-8_source.changes dpkg-buildpackage: info: source package rate4site dpkg-buildpackage: info: source version 3.0.0-8 dpkg-buildpackage: info: source distribution unstable @@ -385,7 +428,7 @@ ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -418,8 +461,8 @@ checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for string... yes checking for iostream... yes checking for size_t... yes @@ -444,7 +487,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/rate4site-3.0.0' make all-recursive make[2]: Entering directory '/build/rate4site-3.0.0' @@ -468,6 +511,7 @@ /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++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o pijAccelerator.o pijAccelerator.cpp /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*, vector > >; _Distance = int; _Tp = vecElem; _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*, std::vector > >' 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*, vector > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': @@ -501,7 +545,8 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o pijAccelerator.o pijAccelerator.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o replacementModel.o replacementModel.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o distribution.o distribution.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 'double computeFDRthreshold(Vdouble&, double, bool)' at someUtil.cpp:702:7: @@ -522,12 +567,12 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o replacementModel.o replacementModel.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o distribution.o distribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o readTree.o readTree.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o errorMsg.o errorMsg.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nucleotide.o nucleotide.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o amino.o amino.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o geneticCodeHolder.o geneticCodeHolder.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o codon.o codon.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, from someUtil.h:7, @@ -690,8 +735,6 @@ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o geneticCodeHolder.o geneticCodeHolder.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o codon.o codon.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o doubleRep.o doubleRep.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o uniDistribution.o uniDistribution.cpp @@ -723,6 +766,7 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o datMatrixHolder.o datMatrixHolder.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nucJC.o nucJC.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, from readDatMatrix.h:6, @@ -731,27 +775,13 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from definitions.h:18, - from pijAccelerator.h:6, - from chebyshevAccelerator.h:6, - from chebyshevAccelerator.cpp:3: -/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>:: - | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o aaJC.o aaJC.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'VVdouble fromWagSandFreqToQ(const VVdouble&, const Vdouble&)' at readDatMatrix.cpp:259:46: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void chebyshevAccelerator::chebft(Vdouble&, int, int, int)' at chebyshevAccelerator.cpp:94:10: -/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1053 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readDatMatrixFromFile(const std::string&, VVdouble&, Vdouble&)' at readDatMatrix.cpp:52:52: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -762,6 +792,16 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gtrModel.o gtrModel.cpp +In file included from /usr/include/c++/12/vector:70, + from definitions.h:18, + from pijAccelerator.h:6, + from chebyshevAccelerator.h:6, + from chebyshevAccelerator.cpp:3: +/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 member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:95:52: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -782,6 +822,12 @@ | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void chebyshevAccelerator::chebft(Vdouble&, int, int, int)' at chebyshevAccelerator.cpp:94:10: +/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1053 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void codonUtility::readCodonUsage(const std::string&, Vdouble&, const codon&)' at codon.cpp:460:19: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); @@ -801,25 +847,37 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nucJC.o nucJC.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o aaJC.o aaJC.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void codonUtility::getCodonUsage(const sequenceContainer&, Vint&, Vdouble&)' at codon.cpp:436:19: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fromQtoPt.o fromQtoPt.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o distanceTable.o distanceTable.cpp +In file included from /usr/include/c++/12/vector:70, + from definitions.h:18, + from replacementModel.h:6, + from gtrModel.h:4, + from gtrModel.cpp:1: +/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 member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static double codonUtility::calcCodonAdaptationIndex(const sequenceContainer&, const Vdouble&, Vdouble&)' at codon.cpp:517:17: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gtrModel.o gtrModel.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fromQtoPt.o fromQtoPt.cpp +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)' at gtrModel.cpp:15:50: +/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1053 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nj.o nj.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, - from replacementModel.h:6, - from gtrModel.h:4, - from gtrModel.cpp:1: + from distanceTable.cpp:3: /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>:: @@ -833,17 +891,17 @@ | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)' at gtrModel.cpp:15:50: + inlined from 'void giveDistanceTable(const distanceMethod*, const sequenceContainer&, VVdouble&, std::vector >&, const std::vector*)' at distanceTable.cpp:12:55: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o njConstrain.o njConstrain.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'VVdouble get1PamFromCountMatrix(const std::vector&, const VVdouble&)' at fromQtoPt.cpp:256:17: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o distanceTable.o distanceTable.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void q2pt::fillFromRateMatrix(const std::vector&, const VVdouble&)' at fromQtoPt.cpp:27:50: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -864,22 +922,16 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nj.o nj.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o numRec.o numRec.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, - from distanceTable.cpp:3: + from nj.h:8, + from nj.cpp:6: /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, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void giveDistanceTable(const distanceMethod*, const sequenceContainer&, VVdouble&, std::vector >&, const std::vector*)' at distanceTable.cpp:12:55: -/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1053 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o njConstrain.o njConstrain.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o numRec.o numRec.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o uniformDistribution.o uniformDistribution.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from numRec.cpp:6: @@ -887,6 +939,12 @@ /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void NJalg::UpdateDistanceTableAndCurrentNodes(std::vector&, VVdouble&, tree::nodeP, tree::nodeP, tree::nodeP, int, int)' at nj.cpp:265:66: +/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1053 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, @@ -902,18 +960,24 @@ /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/vector:70, from definitions.h:18, - from nj.h:8, - from nj.cpp:6: + from uniformDistribution.h:22, + from uniformDistribution.cpp:3: /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, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void NJalg::UpdateDistanceTableAndCurrentNodes(std::vector&, VVdouble&, tree::nodeP, tree::nodeP, tree::nodeP, int, int)' at nj.cpp:265:66: + inlined from 'void uniformDistribution::setUniformParameters(int, double, double)' at uniformDistribution.cpp:33:15: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void uniformDistribution::setUniformParameters(int, double, double)' at uniformDistribution.cpp:35:19: +/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1053 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computePijComponent.o computePijComponent.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 'double performKSTest(const uniformDistribution&, Vdouble&)' at numRec.cpp:465:6: @@ -942,14 +1006,14 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o uniformDistribution.o uniformDistribution.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o stochasticProcess.o stochasticProcess.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeEigenSystem(VVdouble&, VVdouble&, Vdouble&)' at numRec.cpp:443:20: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computePijComponent.o computePijComponent.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o suffStatComponent.o suffStatComponent.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void houseHolder(VVdouble&, VVdouble&)' at numRec.cpp:167:14: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -970,40 +1034,34 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o unObservableData.o unObservableData.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likeDist.o likeDist.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o countTableComponent.o countTableComponent.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, - from uniformDistribution.h:22, - from uniformDistribution.cpp:3: + from computePijComponent.cpp:4: /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, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void uniformDistribution::setUniformParameters(int, double, double)' at uniformDistribution.cpp:33:15: -/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1053 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void uniformDistribution::setUniformParameters(int, double, double)' at uniformDistribution.cpp:35:19: + inlined from 'void computePijHomSpec::resize(int)' at computePijComponent.h:19:48, + inlined from 'void computePijHomSpec::fillPij(double, const stochasticProcess&, int, bool)' at computePijComponent.cpp:14:11: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o stochasticProcess.o stochasticProcess.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o suffStatComponent.o suffStatComponent.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o unObservableData.o unObservableData.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likeDist.o likeDist.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, - from computePijComponent.cpp:4: + from countTableComponent.h:6, + from countTableComponent.cpp:6: /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, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computePijHomSpec::resize(int)' at computePijComponent.h:19:48, - inlined from 'void computePijHomSpec::fillPij(double, const stochasticProcess&, int, bool)' at computePijComponent.cpp:14:11: + inlined from 'void countTableComponentHom::countTableComponentAllocatePlace(int)' at countTableComponent.cpp:20:104: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1013,7 +1071,7 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o countTableComponent.o countTableComponent.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fastStartTree.o fastStartTree.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, from unObservableData.h:4, @@ -1022,30 +1080,14 @@ /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:70, - from definitions.h:18, - from countTableComponent.h:6, - from countTableComponent.cpp:6: -/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>:: - | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestAlpha.o bestAlpha.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'unObservableData::unObservableData(const sequenceContainer&, const stochasticProcess*, gainLossAlphabet, int, int)' at unObservableData.cpp:12:31: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void countTableComponentHom::countTableComponentAllocatePlace(int)' at countTableComponent.cpp:20:104: -/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1053 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fastStartTree.o fastStartTree.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestAlpha.o bestAlpha.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gammaDistribution.o gammaDistribution.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from fastStartTree.cpp:15: @@ -1066,7 +1108,7 @@ /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++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o siteSpecificRate.o siteSpecificRate.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gammaDistribution.o gammaDistribution.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 'std::vector eliminateHalf(std::vector&, sequenceContainer&, stochasticProcess&, std::ostream&, int)' at fastStartTree.cpp:36:6: @@ -1087,206 +1129,207 @@ /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++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o siteSpecificRate.o siteSpecificRate.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputation.o likelihoodComputation.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o recognizeFormat.o recognizeFormat.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bblEM.o bblEM.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, - from bestAlpha.h:6, - from bestAlpha.cpp:6: + from likelihoodComputation.cpp:3: /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:70, from definitions.h:18, - from siteSpecificRate.h:6, - from siteSpecificRate.cpp:3: + from bestAlpha.h:6, + from bestAlpha.cpp:6: /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, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, double)' at siteSpecificRate.cpp:20:15: + inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:394:22: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, double)' at siteSpecificRate.cpp:21:21: + inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:397:30: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:151:15: + inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:402:16: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from definitions.h:18, + from siteSpecificRate.h:6, + from siteSpecificRate.cpp:3: +/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, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:152:13: + inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, double)' at siteSpecificRate.cpp:20:15: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:153:20: + inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, double)' at siteSpecificRate.cpp:21:21: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:154:20: + inlined from 'Vdouble likelihoodComputation::getLofPosPerCat(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&)' at likelihoodComputation.cpp:581:12: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const Vint&, const Vint&, const std::vector&, const std::vector&, const sequenceContainer&, double, double)' at siteSpecificRate.cpp:64:15: + inlined from 'doubleRep likelihoodComputation::getLofPosProportional(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&)' at likelihoodComputation.cpp:203:18: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const Vint&, const Vint&, const std::vector&, const std::vector&, const sequenceContainer&, double, double)' at siteSpecificRate.cpp:65:21: + inlined from 'doubleRep likelihoodComputation::getLofPosProportional(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, double)' at likelihoodComputation.cpp:181:18: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:415:15: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:151:15: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:416:13: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:152:13: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:417:20: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:153:20: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:418:20: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)' at siteSpecificRate.cpp:154:20: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bestAlphasAndBBLProportional::bestAlphasAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double)' at bestAlpha.cpp:129:29: + inlined from 'doubleRep likelihoodComputation::getLofPos(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, unObservableData*)' at likelihoodComputation.cpp:67:18: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bestAlphasAndBBLProportional::bestAlphasAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double)' at bestAlpha.cpp:150:16: + inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const Vint&, const Vint&, const std::vector&, const std::vector&, const sequenceContainer&, double, double)' at siteSpecificRate.cpp:64:15: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from definitions.h:18, - from likelihoodComputation.cpp:3: -/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, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:394:22: + inlined from 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const Vint&, const Vint&, const std::vector&, const std::vector&, const sequenceContainer&, double, double)' at siteSpecificRate.cpp:65:21: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:397:30: + inlined from 'double likelihoodComputation::computeLikelihoodAndLikelihoodPerPosition(const sequenceContainer&, const tree&, const stochasticProcess&, Vdouble&)' at likelihoodComputation.cpp:559:17: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 444 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:380:20: +/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>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:402:16: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:415:15: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRateProportional(int, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double&, double&, double&, double&, double, VVVdouble*)' at siteSpecificRate.cpp:323:33: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:416:13: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'Vdouble likelihoodComputation::getLofPosPerCat(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&)' at likelihoodComputation.cpp:581:12: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:417:20: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'doubleRep likelihoodComputation::getLofPosProportional(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&)' at likelihoodComputation.cpp:203:18: + inlined from 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)' at siteSpecificRate.cpp:418:20: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double likelihoodComputation::getTreeLikelihoodFromUpSpecifcRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalHom&, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:530:20: +/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 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VdoubleRep&, const Vdouble*, unObservableData*)' at likelihoodComputation.cpp:350:20: +/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:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'doubleRep likelihoodComputation::getLofPosProportional(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, double)' at likelihoodComputation.cpp:181:18: + inlined from 'bestAlphasAndBBLProportional::bestAlphasAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double)' at bestAlpha.cpp:129:29: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'doubleRep likelihoodComputation::getLofPos(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, unObservableData*)' at likelihoodComputation.cpp:67:18: + inlined from 'bestAlphasAndBBLProportional::bestAlphasAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double)' at bestAlpha.cpp:150:16: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:291:15: + inlined from 'double likelihoodComputation::getPosteriorOfRatesAndLLPP(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VVdoubleRep&, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:487:70: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:292:13: + inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:138:26: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:293:20: + inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:141:38: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:294:20: + inlined from 'void computeEB_EXP_siteSpecificRateProportional(int, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double&, double&, double&, double&, double, VVVdouble*)' at siteSpecificRate.cpp:323:33: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::computeLikelihoodAndLikelihoodPerPosition(const sequenceContainer&, const tree&, const stochasticProcess&, Vdouble&)' at likelihoodComputation.cpp:559:17: + inlined from 'double likelihoodComputation::getPosteriorOfRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:453:70: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 444 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:380:20: -/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 'double likelihoodComputation::getTreeLikelihoodFromUpSpecifcRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalHom&, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:530:20: -/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 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VdoubleRep&, const Vdouble*, unObservableData*)' at likelihoodComputation.cpp:350:20: -/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>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getPosteriorOfRatesAndLLPP(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VVdoubleRep&, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:487:70: + inlined from 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:291:15: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o recognizeFormat.o recognizeFormat.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bblEM.o bblEM.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:138:26: + inlined from 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:292:13: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:141:38: + inlined from 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:293:20: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double likelihoodComputation::getPosteriorOfRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:453:70: + inlined from 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)' at siteSpecificRate.cpp:294:20: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1294,6 +1337,15 @@ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestGtrModelParams.o bestGtrModelParams.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, + from bblEM.h:5, + from bblEM.cpp:2: +/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>:: + | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o tamura92.o tamura92.cpp +In file included from /usr/include/c++/12/vector:70, + from definitions.h:18, from replacementModel.h:6, from hky.h:6, from hky.cpp:3: @@ -1307,15 +1359,6 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o tamura92.o tamura92.cpp -In file included from /usr/include/c++/12/vector:70, - from definitions.h:18, - from bblEM.h:5, - from bblEM.cpp:2: -/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:70, from definitions.h:18, from replacementModel.h:6, @@ -1332,6 +1375,7 @@ 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestHKYparam.o bestHKYparam.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestTamura92param.o bestTamura92param.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, @@ -1340,6 +1384,8 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o talRandom.o talRandom.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, from bestGtrModelParams.h:6, @@ -1348,7 +1394,14 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestTamura92param.o bestTamura92param.cpp +In file included from /usr/include/c++/12/vector:70, + from definitions.h:18, + from bestTamura92param.h:6, + from bestTamura92param.cpp:3: +/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:70, from definitions.h:18, from bestHKYparam.h:6, @@ -1370,121 +1423,115 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bestGtrModelProportional::bestGtrModelProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)' at bestGtrModelParams.cpp:218:16: + inlined from 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double, double)' at bestTamura92param.cpp:244:16: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bestGtrModelProportional::bestGtrModelProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)' at bestGtrModelParams.cpp:223:18: + inlined from 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double, double)' at bestTamura92param.cpp:250:18: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from definitions.h:18, - from bestTamura92param.h:6, - from bestTamura92param.cpp:3: -/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>:: - | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o talRandom.o talRandom.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeCounts.o computeCounts.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double, double)' at bestTamura92param.cpp:244:16: + inlined from 'bestGtrModelProportional::bestGtrModelProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)' at bestGtrModelParams.cpp:218:16: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double, double)' at bestTamura92param.cpp:250:18: + inlined from 'bestGtrModelProportional::bestGtrModelProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)' at bestGtrModelParams.cpp:223:18: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeCounts.o computeCounts.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeDownAlg.o computeDownAlg.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, - from computeDownAlg.cpp:3: + from computeSubstitutionCounts.h:4, + from computeSubstitutionCounts.cpp:1: /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>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeDownAlg.o computeDownAlg.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeUpAlg.o computeUpAlg.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, - inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'void computeDownAlg::fillComputeDownSpecificRate(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&, double)' at computeDownAlg.cpp:120:19: + inlined from 'void computeSubstitutionCounts::run()' at computeSubstitutionCounts.cpp:38:62: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, - inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'void computeDownAlg::fillComputeDown(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:14:19: + inlined from 'void computeSubstitutionCounts::run()' at computeSubstitutionCounts.cpp:39:63: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from definitions.h:18, - from computeSubstitutionCounts.h:4, - from computeSubstitutionCounts.cpp:1: + from computeDownAlg.cpp:3: /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 member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:225:48: +/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1053 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'void computeDownAlg::fillComputeDown(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:63:19: + inlined from 'void computeDownAlg::fillComputeDownSpecificRate(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&, double)' at computeDownAlg.cpp:120:19: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'void suffStatGlobalGamPos::allocatePlace(int, int, int)' at suffStatComponent.h:147:54, - inlined from 'void computeDownAlg::fillComputeDownNonReversible(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalGamPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:176:30: + inlined from 'void computeDownAlg::fillComputeDown(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:14:19: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from definitions.h:18, - from computeUpAlg.cpp:3: -/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>:: - | ^~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp -In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeSubstitutionCounts::run()' at computeSubstitutionCounts.cpp:38:62: + inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, + inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, + inlined from 'void computeDownAlg::fillComputeDown(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:63:19: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeSubstitutionCounts::run()' at computeSubstitutionCounts.cpp:39:63: + inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:356:43: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:225:48: + inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:357:42: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: +In file included from /usr/include/c++/12/vector:70, + from definitions.h:18, + from computeUpAlg.cpp:3: +/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 member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'void computeUpAlg::fillComputeUpSpecificGlobalRate(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double)' at computeUpAlg.cpp:110:19: + inlined from 'void suffStatGlobalGamPos::allocatePlace(int, int, int)' at suffStatComponent.h:147:54, + inlined from 'void computeDownAlg::fillComputeDownNonReversible(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalGamPos&, const suffStatGlobalHomPos&)' at computeDownAlg.cpp:176:30: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gammaUtilities.o gammaUtilities.cpp +In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'void computeUpAlg::fillComputeUp(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&)' at computeUpAlg.cpp:33:19: + inlined from 'void computeUpAlg::fillComputeUpSpecificGlobalRate(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double)' at computeUpAlg.cpp:110:19: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1496,23 +1543,14 @@ 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:356:43: -/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1053 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:357:42: -/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1053 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'void suffStatGlobalGamPos::allocatePlace(int, int, int)' at suffStatComponent.h:147:54, - inlined from 'void suffStatGlobalGam::allocatePlace(int, int, int, int)' at suffStatComponent.h:193:54: + inlined from 'void computeUpAlg::fillComputeUp(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&)' at computeUpAlg.cpp:33:19: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o treeUtil.o treeUtil.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeUpAlg::fillComputeUpSpecificGlobalRateFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double, std::vector&)' at computeUpAlgFactors.cpp:128:16: @@ -1526,7 +1564,6 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gammaUtilities.o gammaUtilities.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&, std::vector&)' at computeUpAlgFactors.cpp:42:16: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1540,6 +1577,14 @@ 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, + inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, + inlined from 'void suffStatGlobalGamPos::allocatePlace(int, int, int)' at suffStatComponent.h:147:54, + inlined from 'void suffStatGlobalGam::allocatePlace(int, int, int, int)' at suffStatComponent.h:193:54: +/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1053 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, std::vector&)' at computeUpAlgFactors.cpp:84:16: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); @@ -1551,9 +1596,9 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o treeUtil.o treeUtil.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o matrixUtils.o matrixUtils.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, from matrixUtils.h:4, @@ -1562,12 +1607,25 @@ /usr/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 444 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from definitions.h:18, + from simulateJumpsAbstract.h:4, + from simulateCodonsJumps.h:4, + from simulateCodonsJumps.cpp:1: +/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>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readDoubleVecFromFile(Vdouble&, std::string)' at matrixUtils.cpp:198:17: /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/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 444 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void appendVectors(VVdouble&, const VVdouble&)' at matrixUtils.cpp:175:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1587,7 +1645,6 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ludcmp(VVdouble&, Vdouble&, double&)' at matrixUtils.cpp:248:13: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1615,18 +1672,12 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from definitions.h:18, - from simulateJumpsAbstract.h:4, - from simulateCodonsJumps.h:4, - from simulateCodonsJumps.cpp:1: + from computePosteriorExpectationOfSubstitutions.h:13, + from computePosteriorExpectationOfSubstitutions.cpp:1: /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>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, const _Tp&) [with _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:444:5: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 444 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void simulateCodonsJumps::init()' at simulateCodonsJumps.cpp:20:27: @@ -1643,23 +1694,14 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp -In file included from /usr/include/c++/12/vector:70, - from definitions.h:18, - from computePosteriorExpectationOfSubstitutions.h:13, - from computePosteriorExpectationOfSubstitutions.cpp:1: -/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, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void resizeMatrix(std::vector >&, int, int) [with _T = double]' at matrixUtils.h:38:16: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumps.o simulateJumps.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, @@ -1667,6 +1709,10 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumps.o simulateJumps.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o treeIt.o treeIt.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, from computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:1: @@ -1674,20 +1720,13 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o tree.o tree.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void resizeMatrix(std::vector >&, int, int) [with _T = double]' at matrixUtils.h:38:16: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, - inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, - inlined from 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:26:21: -/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1053 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from definitions.h:18, from simulateJumpsAbstract.h:4, @@ -1697,9 +1736,14 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o treeIt.o treeIt.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o tree.o tree.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, + inlined from 'void suffStatGlobalHomPos::allocatePlace(int, int)' at suffStatComponent.h:127:54, + inlined from 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:26:21: +/usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1053 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void simulateJumps::init()' at simulateJumps.cpp:21:27: @@ -1716,7 +1760,6 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, from likelihoodComputationGL.h:4, @@ -1742,6 +1785,8 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likeDistPropEB.o likeDistPropEB.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o phylipFormat.o phylipFormat.cpp In file included from /usr/include/c++/12/vector:70, from definitions.h:18, from bblEM.h:5, @@ -1750,15 +1795,9 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp -In file included from /usr/include/c++/12/vector:70, - from definitions.h:18, - from tree.cpp:2: -/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>:: - | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o phylipFormat.o phylipFormat.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o maseFormat.o maseFormat.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o clustalFormat.o clustalFormat.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fastaFormat.o fastaFormat.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatSpecHomPos::allocatePlace(int)' at suffStatComponent.h:29:13, @@ -1768,29 +1807,33 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from definitions.h:18, + from tree.cpp:2: +/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>:: + | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o molphyFormat.o molphyFormat.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void tree::getTreeDistanceTableAndNames(VVdouble&, std::vector >&) const' at tree.cpp:453:21: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o maseFormat.o maseFormat.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o clustalFormat.o clustalFormat.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fastaFormat.o fastaFormat.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o getRandomWeights.o getRandomWeights.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nexusFormat.o nexusFormat.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void bblEMProportionalEB::allocatePlacePropEB()' at bblEMProportionalEB.cpp:106:31: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, value_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'Vdouble bblEMProportionalEB::compute_bblEMPropEB(int, double, double, const double*)' at bblEMProportionalEB.cpp:41:17: /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o molphyFormat.o molphyFormat.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o getRandomWeights.o getRandomWeights.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o nexusFormat.o nexusFormat.cpp rm -f libphylo.a ar cru libphylo.a alphabet.o sequenceContainer.o sequence.o mulAlphabet.o someUtil.o logFile.o gainLossAlphabet.o pijAccelerator.o replacementModel.o distribution.o readTree.o errorMsg.o nucleotide.o amino.o geneticCodeHolder.o codon.o doubleRep.o evaluateCharacterFreq.o uniDistribution.o generalGammaDistribution.o readDatMatrix.o datMatrixHolder.o chebyshevAccelerator.o nucJC.o aaJC.o gtrModel.o fromQtoPt.o distanceTable.o nj.o njConstrain.o numRec.o uniformDistribution.o computePijComponent.o stochasticProcess.o suffStatComponent.o unObservableData.o likeDist.o countTableComponent.o fastStartTree.o likelihoodComputationFactors.o bestAlpha.o gammaDistribution.o siteSpecificRate.o likelihoodComputation.o recognizeFormat.o bblEM.o hky.o bestGtrModelParams.o tamura92.o bestHKYparam.o bestTamura92param.o talRandom.o computeSubstitutionCounts.o fromCountTableComponentToDistance.o computeCounts.o computeDownAlg.o computeUpAlg.o computeUpAlgFactors.o gammaUtilities.o seqContainerTreeMap.o treeUtil.o matrixUtils.o simulateCodonsJumps.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o multipleStochasticProcess.o simulateJumps.o simulateJumpsAbstract.o treeIt.o likelihoodComputationGL.o tree.o bblEMProportionalEB.o fromCountTableComponentToDistancePropEB.o likeDistPropEB.o bblLSProportionalEB.o phylipFormat.o maseFormat.o clustalFormat.o fastaFormat.o phylipSequentialFormat.o molphyFormat.o getRandomWeights.o nexusFormat.o ar: `u' modifier ignored since `D' is the default (see `U') @@ -1832,15 +1875,15 @@ /usr/include/c++/12/bits/stl_vector.h:1053:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1053 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -Wl,-z,relro -Wl,-z,now -o rate4site rate4site-rate4siteOptions.o rate4site-rate4site.o ../../src/phylogeny/libphylo.a g++ -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -Wl,-z,relro -Wl,-z,now -o rate4site_doublerep rate4siteOptions.o rate4site.o ../../src/phylogeny/libphylo.a +g++ -I../../src/phylogeny/ -g -O2 -ffile-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -Wl,-z,relro -Wl,-z,now -o rate4site rate4site-rate4siteOptions.o rate4site-rate4site.o ../../src/phylogeny/libphylo.a make[3]: Leaving directory '/build/rate4site-3.0.0/src/rate4site' make[3]: Entering directory '/build/rate4site-3.0.0' make[3]: Leaving directory '/build/rate4site-3.0.0' make[2]: Leaving directory '/build/rate4site-3.0.0' make[1]: Leaving directory '/build/rate4site-3.0.0' dh_auto_test - make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 + make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/build/rate4site-3.0.0' Making check in src/phylogeny make[2]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' @@ -1856,14 +1899,14 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/rate4site/ - make -j3 install DESTDIR=/build/rate4site-3.0.0/debian/rate4site AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/rate4site-3.0.0/debian/rate4site AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/rate4site-3.0.0' Making install in src/phylogeny make[2]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' make[3]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' - /bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/lib/arm-linux-gnueabihf' + /usr/bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/lib/arm-linux-gnueabihf' /usr/bin/install -c -m 644 libphylo.a '/build/rate4site-3.0.0/debian/rate4site/usr/lib/arm-linux-gnueabihf' - /bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' + /usr/bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' /usr/bin/install -c -m 644 replacementMatrixSource/mitochondriaAscidian.code replacementMatrixSource/mitochondriaProtozoan.code replacementMatrixSource/nuclearCiliate.code replacementMatrixSource/mitochondriaEchinoderm.code replacementMatrixSource/mitochondriaVertebrate.code replacementMatrixSource/nuclearEuplotid.code replacementMatrixSource/mitochondriaFlatworm.code replacementMatrixSource/mitochondriaYeast.code replacementMatrixSource/nuclearStandard.code replacementMatrixSource/mitochondriaInvertebrate.code replacementMatrixSource/nuclearBlepharisma.code cpREV45.dat.q dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q adrianCodon.dat.q LG.dat.q replacementMatrixSource/cpREV45.dat replacementMatrixSource/dayhoff.dat replacementMatrixSource/jones.dat replacementMatrixSource/mtREV24.dat replacementMatrixSource/wag.dat getopt.h errorMsg.h definitions.h doubleRep.h ConversionUtils.h sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h pijAccelerator.h replacementModel.h distribution.h '/build/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' /usr/bin/install -c -m 644 readTree.h nucleotide.h amino.h geneticCodeHolder.h codon.h evaluateCharacterFreq.h uniDistribution.h generalGammaDistribution.h readDatMatrix.h datMatrixHolder.h chebyshevAccelerator.h nucJC.h aaJC.h gtrModel.h fromQtoPt.h trivialAccelerator.h distanceMethod.h distanceTable.h nj.h njConstrain.h distances2Tree.h numRec.h uniformDistribution.h checkcovFanctors.h likelihoodComputation.h computePijComponent.h stochasticProcess.h suffStatComponent.h unObservableData.h likeDist.h countTableComponent.h jcDistance.h fastStartTree.h checkcovFanctorsWithFactors.h likelihoodComputationFactors.h bestAlpha.h gammaDistribution.h siteSpecificRate.h recognizeFormat.h bblEM.h '/build/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' /usr/bin/install -c -m 644 bestGtrModelParams.h tamura92.h bestHKYparam.h hky.h bestTamura92param.h talRandom.h computeSubstitutionCounts.h fromCountTableComponentToDistance.h computeCounts.h computeDownAlg.h computeUpAlg.h gammaUtilities.h seqContainerTreeMap.h treeUtil.h matrixUtils.h computePosteriorExpectationOfSubstitutions.h computePosteriorExpectationOfSubstitutions_nonReversibleSp.h multipleStochasticProcess.h simulateJumps.h simulateJumpsAbstract.h simulateCodonsJumps.h treeIt.h likelihoodComputationGL.h tree.h bblEMProportionalEB.h fromCountTableComponentToDistancePropEB.h likeDistPropEB.h bblLSProportionalEB.h phylipFormat.h maseFormat.h clustalFormat.h fastaFormat.h phylipSequentialFormat.h molphyFormat.h getRandomWeights.h nexusFormat.h '/build/rate4site-3.0.0/debian/rate4site/usr/include/libphylo' @@ -1873,8 +1916,8 @@ Making install in src/rate4site make[2]: Entering directory '/build/rate4site-3.0.0/src/rate4site' make[3]: Entering directory '/build/rate4site-3.0.0/src/rate4site' - /bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/bin' - /bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/share/man/man1' + /usr/bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/bin' + /usr/bin/mkdir -p '/build/rate4site-3.0.0/debian/rate4site/usr/share/man/man1' /usr/bin/install -c rate4site rate4site_doublerep '/build/rate4site-3.0.0/debian/rate4site/usr/bin' /usr/bin/install -c -m 644 rate4site.1 '/build/rate4site-3.0.0/debian/rate4site/usr/share/man/man1' make[3]: Leaving directory '/build/rate4site-3.0.0/src/rate4site' @@ -1905,8 +1948,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'rate4site-dbgsym' in '../rate4site-dbgsym_3.0.0-8_armhf.deb'. dpkg-deb: building package 'rate4site' in '../rate4site_3.0.0-8_armhf.deb'. +dpkg-deb: building package 'rate4site-dbgsym' in '../rate4site-dbgsym_3.0.0-8_armhf.deb'. dpkg-genbuildinfo --build=binary -O../rate4site_3.0.0-8_armhf.buildinfo dpkg-genchanges --build=binary -O../rate4site_3.0.0-8_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1914,12 +1957,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3244/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3244/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/29878 and its subdirectories -I: Current time: Thu May 11 20:34:57 -12 2023 -I: pbuilder-time-stamp: 1683880497 +I: removing directory /srv/workspace/pbuilder/3244 and its subdirectories +I: Current time: Fri May 12 23:01:33 +14 2023 +I: pbuilder-time-stamp: 1683882093