Diff of the two buildlogs: -- --- b1/build.log 2021-09-07 02:41:35.205917816 +0000 +++ b2/build.log 2021-09-07 02:46:10.668026898 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 6 14:38:11 -12 2021 -I: pbuilder-time-stamp: 1630982291 +I: Current time: Tue Sep 7 16:42:10 +14 2021 +I: pbuilder-time-stamp: 1630982530 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./rate4site_3.0.0-7.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.5yqsV4H6/trustedkeys.kbx': General error -gpgv: Signature made Fri Nov 27 06:08:05 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.fbUVPPNv/trustedkeys.kbx': General error +gpgv: Signature made Sat Nov 28 08:08:05 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,135 +29,169 @@ dpkg-source: info: applying spelling.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/23511/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/10528/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/10528/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/10528/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='6a568e433dd04ccc9dc45c7b62a5e4ef' - 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='23511' - PS1='# ' - PS2='> ' + INVOCATION_ID=35ea2f1351c241968c5f2a47d6683238 + 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=10528 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.uHj9Lyhovz/pbuilderrc_q9h5 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.uHj9Lyhovz/b1 --logfile b1/build.log rate4site_3.0.0-7.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.uHj9Lyhovz/pbuilderrc_cip2 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.uHj9Lyhovz/b2 --logfile b2/build.log rate4site_3.0.0-7.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux jtx1c 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more - -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 20 21:24 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 2021 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/23511/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more + -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 7 16:42 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 21 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 2021 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/10528/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -224,7 +258,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] -Fetched 17.7 MB in 2s (10.7 MB/s) +Fetched 17.7 MB in 6s (3071 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) @@ -364,7 +398,8 @@ Building tag database... -> Finished parsing the build-deps 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_3.0.0-7_source.changes +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_3.0.0-7_source.changes dpkg-buildpackage: info: source package rate4site dpkg-buildpackage: info: source version 3.0.0-7 dpkg-buildpackage: info: source distribution unstable @@ -442,7 +477,7 @@ 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' @@ -459,6 +494,7 @@ 507 | system(sysCall.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gainLossAlphabet.o gainLossAlphabet.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o pijAccelerator.o pijAccelerator.cpp In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from someUtil.cpp:9: @@ -500,9 +536,11 @@ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o replacementModel.o replacementModel.cpp /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1891 | 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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o distribution.o distribution.cpp /usr/include/c++/10/bits/stl_algo.h: In function 'double computeFDRthreshold(Vdouble&, double, bool)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, @@ -517,13 +555,12 @@ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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++/10/vector:72, from definitions.h:18, from someUtil.h:7, @@ -677,12 +714,11 @@ /usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1977 | 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o uniDistribution.o uniDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o generalGammaDistribution.o generalGammaDistribution.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o readDatMatrix.o readDatMatrix.cpp In file included from /usr/include/c++/10/vector:72, from definitions.h:18, from generalGammaDistribution.h:11, @@ -705,31 +741,39 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o readDatMatrix.o readDatMatrix.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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++/10/vector:72, from definitions.h:18, - from pijAccelerator.h:6, - from chebyshevAccelerator.h:6, - from chebyshevAccelerator.cpp:3: + from readDatMatrix.h:6, + from readDatMatrix.cpp:14: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from definitions.h:18, + from codon.h:6, + from codon.cpp:3: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from definitions.h:18, - from pijAccelerator.h:6, - from chebyshevAccelerator.h:6, - from chebyshevAccelerator.cpp:3: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void chebyshevAccelerator::chebft(Vdouble&, int, int, int)': + from codon.h:6, + from codon.cpp:3: +/usr/include/c++/10/bits/stl_vector.h: In static member function 'static void codonUtility::readCodonUsage(const string&, Vdouble&, const codon&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from definitions.h:18, - from readDatMatrix.h:6, - from readDatMatrix.cpp:14: + from pijAccelerator.h:6, + from chebyshevAccelerator.h:6, + from chebyshevAccelerator.cpp:3: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: @@ -742,22 +786,16 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from definitions.h:18, - from codon.h:6, - from codon.cpp:3: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from definitions.h:18, - from codon.h:6, - from codon.cpp:3: -/usr/include/c++/10/bits/stl_vector.h: In static member function 'static void codonUtility::readCodonUsage(const string&, Vdouble&, const codon&)': + from pijAccelerator.h:6, + from chebyshevAccelerator.h:6, + from chebyshevAccelerator.cpp:3: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void chebyshevAccelerator::chebft(Vdouble&, int, int, int)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gtrModel.o gtrModel.cpp /usr/include/c++/10/bits/stl_vector.h: In function 'void readDatMatrixFromFile(const string&, VVdouble&, Vdouble&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); @@ -782,9 +820,6 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o aaJC.o aaJC.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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++/10/vector:72, from definitions.h:18, @@ -795,6 +830,17 @@ /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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++/10/vector:67, + from definitions.h:18, + from replacementModel.h:6, + from gtrModel.h:4, + from gtrModel.cpp:1: +/usr/include/c++/10/bits/stl_vector.h: In constructor 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _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 -fdebug-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++/10/vector:72, from definitions.h:18, from fromQtoPt.cpp:3: @@ -802,6 +848,13 @@ /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from definitions.h:18, + from distanceTable.cpp:3: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In static member function 'static void codonUtility::getCodonUsage(const sequenceContainer&, Vint&, Vdouble&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); @@ -812,15 +865,6 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from definitions.h:18, - from replacementModel.h:6, - from gtrModel.h:4, - from gtrModel.cpp:1: -/usr/include/c++/10/bits/stl_vector.h: In constructor 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from definitions.h:18, from fromQtoPt.cpp:3: /usr/include/c++/10/bits/stl_vector.h: In function 'VVdouble get1PamFromCountMatrix(const std::vector&, const VVdouble&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -839,28 +883,36 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o distanceTable.o distanceTable.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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++/10/vector:72, +In file included from /usr/include/c++/10/vector:67, from definitions.h:18, from distanceTable.cpp:3: +/usr/include/c++/10/bits/stl_vector.h: In function 'void giveDistanceTable(const distanceMethod*, const sequenceContainer&, VVdouble&, std::vector >&, const std::vector*)': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _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 -fdebug-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 -fdebug-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++/10/vector:72, + from definitions.h:18, + from nj.h:8, + from nj.cpp:6: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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++/10/vector:67, from definitions.h:18, - from distanceTable.cpp:3: -/usr/include/c++/10/bits/stl_vector.h: In function 'void giveDistanceTable(const distanceMethod*, const sequenceContainer&, VVdouble&, std::vector >&, const std::vector*)': + from nj.h:8, + from nj.cpp:6: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void NJalg::UpdateDistanceTableAndCurrentNodes(std::vector&, VVdouble&, tree::nodeP, tree::nodeP, tree::nodeP, int, int)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-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++/10/vector:72, from definitions.h:18, - from nj.h:8, - from nj.cpp:6: + from uniformDistribution.h:22, + from uniformDistribution.cpp:3: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: @@ -872,6 +924,17 @@ /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from definitions.h:18, + from uniformDistribution.h:22, + from uniformDistribution.cpp:3: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void uniformDistribution::setUniformParameters(int, double, double)': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from numRec.cpp:6: /usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': @@ -888,14 +951,7 @@ 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/10/vector:67, - from definitions.h:18, - from nj.h:8, - from nj.cpp:6: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void NJalg::UpdateDistanceTableAndCurrentNodes(std::vector&, VVdouble&, tree::nodeP, tree::nodeP, tree::nodeP, int, int)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computePijComponent.o computePijComponent.cpp /usr/include/c++/10/bits/stl_algo.h: In function 'double performKSTest(const uniformDistribution&, Vdouble&)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, @@ -919,8 +975,8 @@ 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 file included from /usr/include/c++/10/vector:67, from definitions.h:18, from numRec.h:13, @@ -931,24 +987,13 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from definitions.h:18, - from uniformDistribution.h:22, - from uniformDistribution.cpp:3: + from computePijComponent.cpp:4: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from definitions.h:18, - from uniformDistribution.h:22, - from uniformDistribution.cpp:3: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void uniformDistribution::setUniformParameters(int, double, double)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o likeDist.o likeDist.cpp /usr/include/c++/10/bits/stl_vector.h: In function 'void houseHolder(VVdouble&, VVdouble&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); @@ -962,16 +1007,6 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o unObservableData.o unObservableData.cpp -In file included from /usr/include/c++/10/vector:72, - from definitions.h:18, - from computePijComponent.cpp:4: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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++/10/vector:67, from definitions.h:18, from computePijComponent.cpp:4: @@ -979,37 +1014,28 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o countTableComponent.o countTableComponent.cpp /usr/include/c++/10/bits/stl_vector.h: In member function 'void computePijHom::fillPij(const tree&, const stochasticProcess&, int, bool)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from definitions.h:18, - from unObservableData.h:4, - from unObservableData.cpp:1: + from countTableComponent.h:6, + from countTableComponent.cpp:6: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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++/10/vector:67, +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/10/vector:72, from definitions.h:18, from unObservableData.h:4, from unObservableData.cpp:1: -/usr/include/c++/10/bits/stl_vector.h: In constructor 'unObservableData::unObservableData(const sequenceContainer&, const stochasticProcess*, gainLossAlphabet, int, int)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from definitions.h:18, - from countTableComponent.h:6, - from countTableComponent.cpp:6: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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++/10/vector:67, from definitions.h:18, from countTableComponent.h:6, @@ -1018,8 +1044,18 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-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 -fdebug-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 -fdebug-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++/10/vector:67, + from definitions.h:18, + from unObservableData.h:4, + from unObservableData.cpp:1: +/usr/include/c++/10/bits/stl_vector.h: In constructor 'unObservableData::unObservableData(const sequenceContainer&, const stochasticProcess*, gainLossAlphabet, int, int)': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _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 -fdebug-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++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from fastStartTree.cpp:15: @@ -1044,7 +1080,6 @@ /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gammaDistribution.o gammaDistribution.cpp /usr/include/c++/10/bits/stl_algo.h: In function 'std::vector eliminateHalf(std::vector&, sequenceContainer&, stochasticProcess&, std::ostream&, int)': /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, @@ -1061,6 +1096,16 @@ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o recognizeFormat.o recognizeFormat.cpp +In file included from /usr/include/c++/10/vector:72, + from definitions.h:18, + from bestAlpha.h:6, + from bestAlpha.cpp:6: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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++/10/vector:72, from definitions.h:18, from siteSpecificRate.h:6, @@ -1069,6 +1114,13 @@ /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from definitions.h:18, + from likelihoodComputation.cpp:3: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from definitions.h:18, from siteSpecificRate.h:6, @@ -1080,50 +1132,6 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In function 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In function 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const Vint&, const Vint&, const std::vector&, const std::vector&, const sequenceContainer&, double, double)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In function 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In function 'void computeEB_EXP_siteSpecificRateProportional(int, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double&, double&, double&, double&, double, VVVdouble*)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from definitions.h:18, - from likelihoodComputation.cpp:3: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from definitions.h:18, from likelihoodComputation.cpp:3: @@ -1145,32 +1153,24 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from definitions.h:18, - from bestAlpha.h:6, - from bestAlpha.cpp:6: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In function 'doubleRep likelihoodComputation::getLofPosProportional(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, double)': +/usr/include/c++/10/bits/stl_vector.h: In function 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, const stochasticProcess&, const tree&, double, VVdouble*, unObservableData*)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In function 'doubleRep likelihoodComputation::getLofPos(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, unObservableData*)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In function 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In function 'doubleRep likelihoodComputation::getLofPosProportional(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, double)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In function 'doubleRep likelihoodComputation::getLofPos(int, const tree&, const sequenceContainer&, const computePijGam&, const stochasticProcess&, unObservableData*)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1186,6 +1186,13 @@ 431 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:431:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/10/bits/stl_vector.h: In function 'double computeML_siteSpecificRate(Vdouble&, Vdouble&, const Vint&, const Vint&, const std::vector&, const std::vector&, const sequenceContainer&, double, double)': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from definitions.h:18, from likelihoodComputation.cpp:3: @@ -1212,11 +1219,23 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In function 'void computeEB_EXP_siteSpecificRate(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const Vint&, const Vint&, const sequenceContainer&, const std::vector&, const std::vector&, double)': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In function 'double likelihoodComputation::getPosteriorOfRatesAndLLPP(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VVdoubleRep&, VdoubleRep&, const Vdouble*)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o recognizeFormat.o recognizeFormat.cpp /usr/include/c++/10/bits/stl_vector.h: In function 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); @@ -1228,9 +1247,34 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bblEM.o bblEM.cpp +/usr/include/c++/10/bits/stl_vector.h: In function 'void computeEB_EXP_siteSpecificRateProportional(int, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double&, double&, double&, double&, double, VVVdouble*)': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In function 'void computeEB_EXP_siteSpecificRateProportional(Vdouble&, Vdouble&, Vdouble&, Vdouble&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const tree&, double, VVVdouble*)': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from definitions.h:18, + from bblEM.h:5, + from bblEM.cpp:2: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o hky.o hky.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestGtrModelParams.o bestGtrModelParams.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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++/10/vector:72, from definitions.h:18, from replacementModel.h:6, @@ -1249,15 +1293,14 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-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++/10/vector:72, +In file included from /usr/include/c++/10/vector:67, from definitions.h:18, from bblEM.h:5, from bblEM.cpp:2: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void suffStatGlobalGamPos::allocatePlace(int, int, int)': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from definitions.h:18, from replacementModel.h:6, @@ -1277,14 +1320,17 @@ 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestHKYparam.o bestHKYparam.cpp -In file included from /usr/include/c++/10/vector:67, +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o bestTamura92param.o bestTamura92param.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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++/10/vector:72, from definitions.h:18, - from bblEM.h:5, - from bblEM.cpp:2: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void suffStatGlobalGamPos::allocatePlace(int, int, int)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + from bestHKYparam.h:6, + from bestHKYparam.cpp:3: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from definitions.h:18, from bestGtrModelParams.h:6, @@ -1293,20 +1339,19 @@ /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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++/10/vector:72, from definitions.h:18, - from bestHKYparam.h:6, - from bestHKYparam.cpp:3: + from bestTamura92param.h:6, + from bestTamura92param.cpp:3: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from definitions.h:18, - from bestGtrModelParams.h:6, - from bestGtrModelParams.cpp:3: -/usr/include/c++/10/bits/stl_vector.h: In constructor '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)': + from bestHKYparam.h:6, + from bestHKYparam.cpp:3: +/usr/include/c++/10/bits/stl_vector.h: In constructor 'bestHkyParamAlphaAndBBLProportional::bestHkyParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1315,9 +1360,9 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from definitions.h:18, - from bestHKYparam.h:6, - from bestHKYparam.cpp:3: -/usr/include/c++/10/bits/stl_vector.h: In constructor 'bestHkyParamAlphaAndBBLProportional::bestHkyParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)': + from bestGtrModelParams.h:6, + from bestGtrModelParams.cpp:3: +/usr/include/c++/10/bits/stl_vector.h: In constructor '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)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1326,14 +1371,12 @@ | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from definitions.h:18, - from bestTamura92param.h:6, - from bestTamura92param.cpp:3: + from computeSubstitutionCounts.h:4, + from computeSubstitutionCounts.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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++/10/vector:67, from definitions.h:18, from bestTamura92param.h:6, @@ -1346,23 +1389,39 @@ 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp +In file included from /usr/include/c++/10/vector:67, + from definitions.h:18, + from computeSubstitutionCounts.h:4, + from computeSubstitutionCounts.cpp:1: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeUpAlg.o computeUpAlg.cpp +/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from definitions.h:18, - from computeSubstitutionCounts.h:4, - from computeSubstitutionCounts.cpp:1: + from computeDownAlg.cpp:3: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from definitions.h:18, - from computeDownAlg.cpp:3: + from computeUpAlg.cpp:3: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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++/10/vector:67, from definitions.h:18, from computeDownAlg.cpp:3: @@ -1370,7 +1429,6 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeUpAlg.o computeUpAlg.cpp /usr/include/c++/10/bits/stl_vector.h: In member function 'void computeDownAlg::fillComputeDown(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&, const suffStatGlobalHomPos&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); @@ -1379,37 +1437,25 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from definitions.h:18, - from computeSubstitutionCounts.h:4, - from computeSubstitutionCounts.cpp:1: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)': +/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeSubstitutionCounts::run()': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeDownAlg::fillComputeDownNonReversible(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalGamPos&, const suffStatGlobalHomPos&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, +In file included from /usr/include/c++/10/vector:67, from definitions.h:18, from computeUpAlg.cpp:3: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp -/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)': +/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeUpAlg::fillComputeUpSpecificGlobalRate(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeDownAlg::fillComputeDownNonReversible(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalGamPos&, const suffStatGlobalHomPos&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from definitions.h:18, - from computeUpAlg.cpp:3: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeUpAlg::fillComputeUpSpecificGlobalRate(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double)': +/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeUpAlg::fillComputeUp(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1420,10 +1466,8 @@ /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeUpAlg::fillComputeUp(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gammaUtilities.o gammaUtilities.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp In file included from /usr/include/c++/10/vector:67, from definitions.h:18, from computeUpAlgFactors.cpp:3: @@ -1434,10 +1478,7 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void computeSubstitutionCounts::run()': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In member function 'void suffStatGlobalGam::allocatePlace(int, int, int, int)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1448,10 +1489,7 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'void suffStatGlobalGam::allocatePlace(int, int, int, int)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o treeUtil.o treeUtil.cpp /usr/include/c++/10/bits/stl_vector.h: In member function 'void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, std::vector&)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); @@ -1459,11 +1497,9 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o gammaUtilities.o gammaUtilities.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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++/10/vector:72, from definitions.h:18, from matrixUtils.h:4, @@ -1537,6 +1573,22 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from definitions.h:18, + from computePosteriorExpectationOfSubstitutions.h:13, + from computePosteriorExpectationOfSubstitutions.cpp:1: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from definitions.h:18, + from computePosteriorExpectationOfSubstitutions.h:13, + from computePosteriorExpectationOfSubstitutions.cpp:1: +/usr/include/c++/10/bits/stl_vector.h: In function 'void resizeMatrix(std::vector >&, int, int) [with _T = double]': +/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 980 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from definitions.h:18, from simulateJumpsAbstract.h:4, @@ -1552,26 +1604,15 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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++/10/vector:72, - from definitions.h:18, - from computePosteriorExpectationOfSubstitutions.h:13, - from computePosteriorExpectationOfSubstitutions.cpp:1: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumps.o simulateJumps.cpp -In file included from /usr/include/c++/10/vector:67, - from definitions.h:18, - from computePosteriorExpectationOfSubstitutions.h:13, - from computePosteriorExpectationOfSubstitutions.cpp:1: -/usr/include/c++/10/bits/stl_vector.h: In function 'void resizeMatrix(std::vector >&, int, int) [with _T = double]': +/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void computePosteriorExpectationOfSubstitutions::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp +g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o treeIt.o treeIt.cpp In file included from /usr/include/c++/10/vector:72, from definitions.h:18, from computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:1: @@ -1579,10 +1620,8 @@ /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void computePosteriorExpectationOfSubstitutions::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)': -/usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 980 | _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 -fdebug-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 -fdebug-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++/10/vector:72, from definitions.h:18, from simulateJumpsAbstract.h:4, @@ -1599,13 +1638,23 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp /usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-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 -fdebug-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 -fdebug-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++/10/vector:72, + from definitions.h:18, + from likelihoodComputationGL.h:4, + from likelihoodComputationGL.cpp:1: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 509 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:431:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 431 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from definitions.h:18, from simulateJumpsAbstract.h:4, @@ -1621,20 +1670,6 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o tree.o tree.cpp -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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++/10/vector:72, - from definitions.h:18, - from likelihoodComputationGL.h:4, - from likelihoodComputationGL.cpp:1: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 509 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:431:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 431 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from definitions.h:18, from likelihoodComputationGL.h:4, @@ -1648,6 +1683,9 @@ 980 | _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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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++/10/vector:72, from definitions.h:18, from bblEM.h:5, @@ -1657,8 +1695,9 @@ 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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++/10/vector:72, from definitions.h:18, from tree.cpp:2: @@ -1666,25 +1705,25 @@ /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wno-deprecated -I../../src -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o getRandomWeights.o getRandomWeights.cpp In file included from /usr/include/c++/10/vector:67, from definitions.h:18, - from bblEM.h:5, - from bblEMProportionalEB.cpp:2: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void suffStatGlobalGamProportionalPos::allocatePlace(int, int, int, int)': + from tree.cpp:2: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void tree::getTreeDistanceTableAndNames(VVdouble&, std::vector >&) const': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-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 -fdebug-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 file included from /usr/include/c++/10/vector:67, from definitions.h:18, - from tree.cpp:2: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void tree::getTreeDistanceTableAndNames(VVdouble&, std::vector >&) const': + from bblEM.h:5, + from bblEMProportionalEB.cpp:2: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void suffStatGlobalGamProportionalPos::allocatePlace(int, int, int, int)': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-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 -fdebug-prefix-map=/build/rate4site-3.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++98 -g -c -o fastaFormat.o fastaFormat.cpp /usr/include/c++/10/bits/stl_vector.h: In member function 'void bblEMProportionalEB::allocatePlacePropEB()': /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); @@ -1693,10 +1732,6 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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') @@ -1742,15 +1777,15 @@ /usr/include/c++/10/bits/stl_vector.h:980:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 980 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -I../../src/phylogeny/ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 VERBOSE=1 + make -j4 check 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' @@ -1766,7 +1801,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - 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' @@ -1824,12 +1859,14 @@ 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/10528/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/10528/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/23511 and its subdirectories -I: Current time: Mon Sep 6 14:41:31 -12 2021 -I: pbuilder-time-stamp: 1630982491 +I: removing directory /srv/workspace/pbuilder/10528 and its subdirectories +I: Current time: Tue Sep 7 16:46:06 +14 2021 +I: pbuilder-time-stamp: 1630982766