Diff of the two buildlogs: -- --- b1/build.log 2023-05-15 19:21:28.138093623 +0000 +++ b2/build.log 2023-05-15 19:31:06.664733204 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 15 07:13:35 -12 2023 -I: pbuilder-time-stamp: 1684178015 +I: Current time: Mon Jun 17 15:44:32 +14 2024 +I: pbuilder-time-stamp: 1718588672 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./fastml_3.11.orig.tar.gz] I: copying [./fastml_3.11-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Dec 17 02:38:59 2020 -12 +gpgv: Signature made Fri Dec 18 04:38:59 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -35,135 +35,167 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/631674/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3628022/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 17 15:44 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3628022/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3628022/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a7eb21da58ec44869baa282a7ca0fa49' - 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='631674' - PS1='# ' - PS2='> ' + INVOCATION_ID=8c044ec0d12f4a53ab324bf84e78dc90 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + 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=3628022 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.RMWgvTyC/pbuilderrc_mGOU --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RMWgvTyC/b1 --logfile b1/build.log fastml_3.11-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.RMWgvTyC/pbuilderrc_HanF --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RMWgvTyC/b2 --logfile b2/build.log --extrapackages usrmerge fastml_3.11-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/631674/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jun 17 15:44 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/3628022/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -229,7 +261,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] -Fetched 18.7 MB in 3s (6210 kB/s) +Fetched 18.7 MB in 1s (21.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) @@ -363,8 +395,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/fastml-3.11/ && 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 > ../fastml_3.11-3_source.changes +I: user script /srv/workspace/pbuilder/3628022/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/3628022/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/fastml-3.11/ && 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 > ../fastml_3.11-3_source.changes dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.11-3 dpkg-buildpackage: info: source distribution unstable @@ -376,7 +419,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/fastml-3.11' dh_auto_clean - make -j15 clean + make -j16 clean make[2]: Entering directory '/build/fastml-3.11' cd libs;make clean cd programs;make clean @@ -385,20 +428,20 @@ make[3]: Entering directory '/build/fastml-3.11/programs' cd fastml && make clean cd gainLoss && make clean -cd indelCoder && make clean +make[4]: Entering directory '/build/fastml-3.11/libs/phylogeny' +rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Entering directory '/build/fastml-3.11/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o -make[4]: Entering directory '/build/fastml-3.11/libs/phylogeny' +cd indelCoder && make clean +make[4]: Leaving directory '/build/fastml-3.11/programs/fastml' make[4]: Entering directory '/build/fastml-3.11/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o -rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o -make[4]: Leaving directory '/build/fastml-3.11/programs/fastml' -make[4]: Entering directory '/build/fastml-3.11/programs/indelCoder' -rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o -make[4]: Leaving directory '/build/fastml-3.11/programs/gainLoss' make[4]: Leaving directory '/build/fastml-3.11/libs/phylogeny' +make[4]: Entering directory '/build/fastml-3.11/programs/indelCoder' make[3]: Leaving directory '/build/fastml-3.11/libs' +rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Leaving directory '/build/fastml-3.11/programs/indelCoder' +make[4]: Leaving directory '/build/fastml-3.11/programs/gainLoss' make[3]: Leaving directory '/build/fastml-3.11/programs' make[2]: Leaving directory '/build/fastml-3.11' rm -f libs/phylogeny/make.dep \ @@ -413,7 +456,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j15 "INSTALL=install --strip-program=true" + make -j16 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/fastml-3.11' cd libs;make all make[2]: Entering directory '/build/fastml-3.11/libs' @@ -437,6 +480,12 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp +bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)': +bestAlpha.cpp:371:17: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] + 371 | MDOUBLE oldA=0; + | ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp bestAlphaManyTrees.cpp: In function 'void bestAlpha::optimizeAlphaNG_EM_PROP_n_alpha(tree&, std::vector&, std::vector&, const std::vector*>*, std::vector&, double&, int, double)': bestAlphaManyTrees.cpp:184:17: warning: variable 'ax' set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha @@ -447,12 +496,6 @@ bestAlphaManyTrees.cpp:184:23: warning: variable 'cx' set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp -bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)': -bestAlpha.cpp:371:17: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] - 371 | MDOUBLE oldA=0; - | ^~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o clustalFormat.o clustalFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp @@ -468,8 +511,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp In file included from computeSubstitutionCounts.cpp:1: computeSubstitutionCounts.h: In constructor 'computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer&, const tree&, multipleStochasticProcess*, std::string&, VVVdouble&, int, double, bool)': computeSubstitutionCounts.h:57:19: warning: 'computeSubstitutionCounts::_LpostPerSpPerCat' will be initialized after [-Wreorder] @@ -490,11 +531,16 @@ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 15 | computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp In file included from /usr/include/c++/12/iostream:39, from readTree.h:6, from tree.h:7, @@ -527,12 +573,10 @@ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:25: note: 'Down' was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3, inlined from 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:39:108: @@ -563,8 +607,10 @@ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:25: note: 'Down' was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp In file included from fromCountTableComponentToDistancePropEB.cpp:3: fromCountTableComponentToDistancePropEB.h: In constructor 'fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB(const std::vector >&, int, multipleStochasticProcess*, const gammaDistribution*, double, double)': fromCountTableComponentToDistancePropEB.h:29:19: warning: 'fromCountTableComponentToDistancePropEB::_nodeID' will be initialized after [-Wreorder] @@ -576,9 +622,6 @@ fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] 6 | fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp @@ -599,12 +642,12 @@ goldmanYangModel.cpp:18:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] 18 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): | ^~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp likeDist.cpp: In instantiation of 'double myNRmethod(double, double, double, regF, dF, double, int, int&) [with regF = C_evalLikeDist_d; dF = C_evalLikeDist_d2]': likeDist.cpp:269:22: required from here likeDist.cpp:210:13: warning: variable 'oldIntervalSize' set but not used [-Wunused-but-set-variable] 210 | MDOUBLE oldIntervalSize = currentIntervalSize; | ^~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o molphyFormat.o molphyFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp @@ -613,6 +656,7 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] 306 | //* for (i=1;igetNumberOfSons()+2); // both s1 and s2 should have been skiped | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readTree.o readTree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o recognizeFormat.o recognizeFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModel.o replacementModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o searchStatus.o searchStatus.cpp @@ -642,11 +685,11 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o siteSpecificRate.o siteSpecificRate.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o split.o split.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp sequence.cpp: In constructor 'sequence::sequence(const sequence&, const alphabet*)': sequence.cpp:76:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 76 | || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp sequenceContainer.cpp: In member function 'void sequenceContainer::removeGapPositions()': sequenceContainer.cpp:187:14: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] 187 | bool gapCol; @@ -672,7 +715,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp tree.cpp: In constructor 'tree::tree(const std::string&)': tree.cpp:180:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 180 | if (in.is_open()) @@ -680,9 +722,8 @@ tree.cpp:182:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 182 | create_names_to_internal_nodes(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp treeUtil.cpp: In function 'std::vector getNexusTreesFromFile(const std::string&)': treeUtil.cpp:371:32: warning: variable 'itStrStart' set but not used [-Wunused-but-set-variable] 371 | string::const_iterator itStrStart = it->begin(); @@ -690,6 +731,8 @@ treeUtil.cpp:372:32: warning: variable 'itStrEnd' set but not used [-Wunused-but-set-variable] 372 | string::const_iterator itStrEnd = it->end(); | ^~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp @@ -700,6 +743,7 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp In file included from distanceBasedSeqs2Tree.cpp:12: bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] @@ -711,7 +755,6 @@ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp @@ -759,7 +802,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp In file included from computeJumps.cpp:1: computeJumps.h: In constructor 'computeJumps::gFunc::gFunc(double, double, double)': computeJumps.h:59:25: warning: 'computeJumps::gFunc::_Lambda2' will be initialized after [-Wreorder] @@ -771,18 +813,27 @@ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] 256 | computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) | ^~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)': seqeuncesFilter.cpp:141:25: warning: unused variable 'pAlph' [-Wunused-variable] 141 | const alphabet* pAlph = sc.getAlphabet(); | ^~~~~ +In file included from GamMixtureOptimizer.cpp:3: +optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': +optGammaMixtureEM.h:76:25: warning: unused variable 'res1' [-Wunused-variable] + 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); + | ^~~~ +optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const': +optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable] + 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); + | ^~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp suffStatGammaMixture.cpp: In member function 'void suffStatGammaMixture::computeStatistics()': suffStatGammaMixture.cpp:123:33: warning: variable 'Exp_Rk' set but not used [-Wunused-but-set-variable] 123 | MDOUBLE Exp_Rk, Exp_LogRk, sum; | ^~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp suffStatGammaMixture.cpp: In member function 'double suffStatGammaMixture::computeQ()': suffStatGammaMixture.cpp:224:25: warning: unused variable 'first' [-Wunused-variable] 224 | MDOUBLE first = _MkVec[comp] * log(P_k); @@ -802,16 +853,8 @@ suffStatGammaMixture.cpp:216:17: warning: variable 'res2' set but not used [-Wunused-but-set-variable] 216 | MDOUBLE res2 = 0.0; | ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp -In file included from GamMixtureOptimizer.cpp:3: -optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': -optGammaMixtureEM.h:76:25: warning: unused variable 'res1' [-Wunused-variable] - 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); - | ^~~~ -optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const': -optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable] - 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); - | ^~~~~~~~ In file included from optGammaMixtureEM.cpp:1: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': optGammaMixtureEM.h:76:25: warning: unused variable 'res1' [-Wunused-variable] @@ -821,6 +864,8 @@ optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable] 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); | ^~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp mixtureDistribution.cpp: In member function 'virtual const double mixtureDistribution::rates(int) const': mixtureDistribution.cpp:221:40: warning: 'componentNum' may be used uninitialized [-Wmaybe-uninitialized] 221 | return _components[componentNum]->rates(categoryInComponent) * _globalRate; @@ -868,8 +913,6 @@ seqeuncesFilter.cpp:165:13: note: 'refID' was declared here 165 | int refID; | ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp @@ -1121,13 +1164,13 @@ make[2]: Entering directory '/build/fastml-3.11/programs' cd fastml && make all cd gainLoss && make all +make[3]: Entering directory '/build/fastml-3.11/programs/fastml' +making depend cd indelCoder && make all make[3]: Entering directory '/build/fastml-3.11/programs/gainLoss' -make[3]: Entering directory '/build/fastml-3.11/programs/fastml' making depend make[3]: Entering directory '/build/fastml-3.11/programs/indelCoder' making depend -making depend g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoder.o indelCoder.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp @@ -1143,6 +1186,7 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bb_options.o bb_options.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp character.cpp: In member function 'int character::getLongestGapStIndex()': character.cpp:28:16: warning: 'longestGapStIndex' may be used uninitialized [-Wmaybe-uninitialized] 28 | return longestGapStIndex; @@ -1150,6 +1194,17 @@ character.cpp:17:13: note: 'longestGapStIndex' was declared here 17 | int longestGapStIndex; | ^~~~~~~~~~~~~~~~~ +In file included from bbReport.cpp:1: +bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': +bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] + 14 | const string& _reportFileName; + | ^~~~~~~~~~~~~~~ +bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] + 13 | const int _minNumOfNodesToVisit; + | ^~~~~~~~~~~~~~~~~~~~~ +bbReport.h:10:18: warning: when initialized here [-Wreorder] + 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) + | ^~~~~~~~~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h: In constructor 'bb_options::bb_options(int&, char**)': bb_options.h:49:16: warning: 'bb_options::reportFile' will be initialized after [-Wreorder] @@ -1228,10 +1283,6 @@ indelCoder.cpp:422:13: warning: unused variable 'gapNum' [-Wunused-variable] 422 | int gapNum = 1; | ^~~~~~ -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ indelCoder.cpp: In member function 'void indelCoder::printIndelSummary()': indelCoder.cpp:587:14: warning: unused variable 'isSIC' [-Wunused-variable] 587 | bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; @@ -1239,24 +1290,10 @@ indelCoder.cpp:597:13: warning: unused variable 'seqLeng' [-Wunused-variable] 597 | int seqLeng = _sc.seqLen(); | ^~~~~~~ -character.cpp: In member function 'void character::checkForTriangleInequality(int, int)': -character.cpp:6:70: warning: 'longestGapStIndex' may be used uninitialized [-Wmaybe-uninitialized] - 6 | if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][longestGapStIndex]){ - | ^ -character.cpp:17:13: note: 'longestGapStIndex' was declared here - 17 | int longestGapStIndex; - | ^~~~~~~~~~~~~~~~~ -In file included from bbNodeOrderAlg.cpp:1: -bbNodeOrderAlg.h: In constructor 'bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)': -bbNodeOrderAlg.h:33:34: warning: 'bbNodeOrderAlg::_sc' will be initialized after [-Wreorder] - 33 | const sequenceContainer& _sc; - | ^~~ -bbNodeOrderAlg.h:32:30: warning: 'const computePijGam& bbNodeOrderAlg::_cpij' [-Wreorder] - 32 | const computePijGam& _cpij; - | ^~~~~ -bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] - 8 | bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, - | ^~~~~~~~~~~~~~ +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] + 62 | static const string usege_splash_screen() { + | ^~~~~~~~~~~~~~~~~~~ In file included from bbEvaluateSpecificAV.cpp:1: bbEvaluateSpecificAV.h: In constructor 'bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&)': bbEvaluateSpecificAV.h:34:34: warning: 'bbEvaluateSpecificAV::_sc' will be initialized after [-Wreorder] @@ -1268,6 +1305,17 @@ bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] 3 | bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, | ^~~~~~~~~~~~~~~~~~~~ +bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': +bbEvaluateSpecificAV.cpp:65:33: warning: unused variable 'rate' [-Wunused-variable] + 65 | MDOUBLE rate = _sp.rates(categor); // the r. + | ^~~~ +character.cpp: In member function 'void character::checkForTriangleInequality(int, int)': +character.cpp:6:70: warning: 'longestGapStIndex' may be used uninitialized [-Wmaybe-uninitialized] + 6 | if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][longestGapStIndex]){ + | ^ +character.cpp:17:13: note: 'longestGapStIndex' was declared here + 17 | int longestGapStIndex; + | ^~~~~~~~~~~~~~~~~ In file included from bbAlg.h:8, from bbAlg.cpp:1: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': @@ -1280,11 +1328,19 @@ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ -bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': -bbEvaluateSpecificAV.cpp:65:33: warning: unused variable 'rate' [-Wunused-variable] - 65 | MDOUBLE rate = _sp.rates(categor); // the r. - | ^~~~ -In file included from bbReport.cpp:1: +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp +bbReport.h: In constructor 'BandBReport::BandBReport(const std::string&, int, int)': +bbReport.h:53:23: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder] + 53 | const string& _reportFileName; + | ^~~~~~~~~~~~~~~ +bbReport.h:51:19: warning: 'const int BandBReport::_position' [-Wreorder] + 51 | const int _position; + | ^~~~~~~~~ +bbReport.cpp:10:1: warning: when initialized here [-Wreorder] + 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : + | ^~~~~~~~~~~ +In file included from bbAlg.h:8, + from fastml.cpp:254: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] 14 | const string& _reportFileName; @@ -1295,7 +1351,22 @@ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp +In file included from bbNodeOrderAlg.cpp:1: +bbNodeOrderAlg.h: In constructor 'bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)': +bbNodeOrderAlg.h:33:34: warning: 'bbNodeOrderAlg::_sc' will be initialized after [-Wreorder] + 33 | const sequenceContainer& _sc; + | ^~~ +bbNodeOrderAlg.h:32:30: warning: 'const computePijGam& bbNodeOrderAlg::_cpij' [-Wreorder] + 32 | const computePijGam& _cpij; + | ^~~~~ +bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] + 8 | bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, + | ^~~~~~~~~~~~~~ +In file included from bbEvaluateSpecificAV.h:4: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] + 62 | static const string usege_splash_screen() { + | ^~~~~~~~~~~~~~~~~~~ bbAlg.h: In constructor 'bbAlg::bbAlg(const tree&, std::vector&, const sequenceContainer&, boundMethod, const std::string&, double, const distribution*)': bbAlg.h:61:23: warning: 'bbAlg::_reportFileName' will be initialized after [-Wreorder] 61 | const string& _reportFileName; @@ -1315,48 +1386,29 @@ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] 7 | bbAlg::bbAlg(const tree& et, | ^~~~~ -In file included from bbAlg.h:8, - from fastml.cpp:254: -bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': -bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] - 14 | const string& _reportFileName; - | ^~~~~~~~~~~~~~~ -bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] - 13 | const int _minNumOfNodesToVisit; - | ^~~~~~~~~~~~~~~~~~~~~ -bbReport.h:10:18: warning: when initialized here [-Wreorder] - 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) - | ^~~~~~~~~~~~~~~~~ -In file included from bbfindBestAVDynProg.h:5, - from bbfindBestAVDynProg.cpp:1: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp -In file included from bbEvaluateSpecificAV.h:4: +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp +computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': +computeMarginalReconstruction.cpp:67:25: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] + 67 | MDOUBLE likelihoodOfPos = 0; + | ^~~~~~~~~~~~~~~ +computeMarginalReconstruction.cpp:45:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] + 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp +In file included from mainbb.h:4, + from fastml.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp -In file included from bbNodeOrderAlg.h:5: -bb_options.h: At global scope: +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp +In file included from bbfindBestAVDynProg.h:5, + from bbfindBestAVDynProg.cpp:1: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp -bbReport.h: In constructor 'BandBReport::BandBReport(const std::string&, int, int)': -bbReport.h:53:23: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder] - 53 | const string& _reportFileName; - | ^~~~~~~~~~~~~~~ -bbReport.h:51:19: warning: 'const int BandBReport::_position' [-Wreorder] - 51 | const int _position; - | ^~~~~~~~~ -bbReport.cpp:10:1: warning: when initialized here [-Wreorder] - 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : - | ^~~~~~~~~~~ -In file included from mainbb.h:4, - from fastml.cpp:1: +In file included from bbNodeOrderAlg.h:5: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { @@ -1367,21 +1419,11 @@ bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp -computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': -computeMarginalReconstruction.cpp:67:25: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] - 67 | MDOUBLE likelihoodOfPos = 0; - | ^~~~~~~~~~~~~~~ -computeMarginalReconstruction.cpp:45:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] - 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': jointNoGamma.cpp:23:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] 23 | MDOUBLE totalLikelihoodOfReconstruction = 0; @@ -1390,29 +1432,7 @@ jointNoGamma.cpp:108:33: warning: unused variable 'maxL' [-Wunused-variable] 108 | MDOUBLE maxL = VERYSMALL; | ^~~~ -In file included from bbAlg.h:8, - from mainbb.cpp:5: -bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': -bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] - 14 | const string& _reportFileName; - | ^~~~~~~~~~~~~~~ -bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] - 13 | const int _minNumOfNodesToVisit; - | ^~~~~~~~~~~~~~~~~~~~~ -bbReport.h:10:18: warning: when initialized here [-Wreorder] - 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) - | ^~~~~~~~~~~~~~~~~ -In file included from mainbb.cpp:31: -../../libs/phylogeny/bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': -../../libs/phylogeny/bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] - 175 | stochasticProcess& _sp; - | ^~~ -../../libs/phylogeny/bestGtrModelParams.h:173:34: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] - 173 | const gammaDistribution* _pProportionDist; - | ^~~~~~~~~~~~~~~~ -../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] - 162 | C_evalGTRParamProportional( const GTRParam param, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp In file included from gainLossUtils.cpp:19: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] @@ -1435,69 +1455,17 @@ gainLossUtils.cpp:481:17: warning: variable 'normFactor' set but not used [-Wunused-but-set-variable] 481 | MDOUBLE normFactor; | ^~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': gainLossUtils.cpp:788:17: warning: unused variable 'scale' [-Wunused-variable] 788 | MDOUBLE scale; | ^~~~~ -In file included from gainLoss.h:35, - from gainLoss.cpp:20: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLossModel.cpp:17: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModel::gainLossModel(double, Vdouble, bool, bool, bool, bool)': -gainLossModel.h:108:17: warning: 'gainLossModel::_gain' will be initialized after [-Wreorder] - 108 | MDOUBLE _gain; // _Q[0][1] - | ^~~~~ -gainLossModel.h:105:17: warning: 'Vdouble gainLossModel::_freq' [-Wreorder] - 105 | Vdouble _freq; - | ^~~~~ -gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] - 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): - | ^~~~~~~~~~~~~ -gainLossModel.h:112:14: warning: 'gainLossModel::_isRootFreqEQstationary' will be initialized after [-Wreorder] - 112 | bool _isRootFreqEQstationary; - | ^~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h:111:14: warning: 'bool gainLossModel::_isReversible' [-Wreorder] - 111 | bool _isReversible; - | ^~~~~~~~~~~~~ -gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] - 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): - | ^~~~~~~~~~~~~ -gainLossModel.h:114:14: warning: 'gainLossModel::_isHGT_with_Q' will be initialized after [-Wreorder] - 114 | bool _isHGT_with_Q; - | ^~~~~~~~~~~~~ -gainLossModel.h:110:15: warning: 'q2pt* gainLossModel::_q2pt' [-Wreorder] - 110 | q2pt *_q2pt; // dont use q2p - | ^~~~~ -gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] - 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): - | ^~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp In file included from optimizeGainLossModel.h:27, from optimizeGainLossModel.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ @@ -1514,39 +1482,12 @@ optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] 20 | optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, | ^~~~~~~~~~~~~~~~~~~~~ -In file included from optimizeGainLossModelVV.h:27, - from optimizeGainLossModelVV.cpp:17: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp -optimizeGainLossModelVV.h: In constructor 'optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)': -optimizeGainLossModelVV.h:82:18: warning: 'optimizeGainLossModelVV::_weightsUniqPatterns' will be initialized after [-Wreorder] - 82 | Vdouble* _weightsUniqPatterns; - | ^~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModelVV.h:81:27: warning: 'unObservableData* optimizeGainLossModelVV::_unObservableData_p' [-Wreorder] - 81 | unObservableData* _unObservableData_p; - | ^~~~~~~~~~~~~~~~~~~ -optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] - 25 | optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, - | ^~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp optimizeGainLossModel.cpp:85:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] 85 | MDOUBLE sumPijQij; | ^~~~~~~~~ -optimizeGainLossModelVV.cpp:258:41: warning: unused variable 'currentlogL' [-Wunused-variable] - 258 | MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); - | ^~~~~~~~~~~ -optimizeGainLossModelVV.cpp:76:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] - 76 | MDOUBLE sumPijQij; - | ^~~~~~~~~ -In file included from siteSpecificGL.cpp:24: +In file included from gainLoss.h:35, + from gainLoss.cpp:20: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] @@ -1585,6 +1526,18 @@ bblLS.h:152:18: warning: when initialized here [-Wreorder] 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from bbAlg.h:8, + from mainbb.cpp:5: +bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': +bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] + 14 | const string& _reportFileName; + | ^~~~~~~~~~~~~~~ +bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] + 13 | const int _minNumOfNodesToVisit; + | ^~~~~~~~~~~~~~~~~~~~~ +bbReport.h:10:18: warning: when initialized here [-Wreorder] + 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) + | ^~~~~~~~~~~~~~~~~ gainLoss.h: In constructor 'gainLoss::gainLoss()': gainLoss.h:266:28: warning: 'gainLoss::_unObservableData_p' will be initialized after [-Wreorder] 266 | unObservableData* _unObservableData_p; @@ -1617,6 +1570,84 @@ gainLoss.cpp:604:14: warning: unused variable 'missigDataChar' [-Wunused-variable] 604 | char missigDataChar = -2; | ^~~~~~~~~~~~~~ +In file included from optimizeGainLossModelVV.h:27, + from optimizeGainLossModelVV.cpp:17: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +optimizeGainLossModelVV.h: In constructor 'optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)': +optimizeGainLossModelVV.h:82:18: warning: 'optimizeGainLossModelVV::_weightsUniqPatterns' will be initialized after [-Wreorder] + 82 | Vdouble* _weightsUniqPatterns; + | ^~~~~~~~~~~~~~~~~~~~ +optimizeGainLossModelVV.h:81:27: warning: 'unObservableData* optimizeGainLossModelVV::_unObservableData_p' [-Wreorder] + 81 | unObservableData* _unObservableData_p; + | ^~~~~~~~~~~~~~~~~~~ +optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] + 25 | optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from gainLossModel.cpp:17: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModel::gainLossModel(double, Vdouble, bool, bool, bool, bool)': +gainLossModel.h:108:17: warning: 'gainLossModel::_gain' will be initialized after [-Wreorder] + 108 | MDOUBLE _gain; // _Q[0][1] + | ^~~~~ +gainLossModel.h:105:17: warning: 'Vdouble gainLossModel::_freq' [-Wreorder] + 105 | Vdouble _freq; + | ^~~~~ +gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] + 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): + | ^~~~~~~~~~~~~ +gainLossModel.h:112:14: warning: 'gainLossModel::_isRootFreqEQstationary' will be initialized after [-Wreorder] + 112 | bool _isRootFreqEQstationary; + | ^~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h:111:14: warning: 'bool gainLossModel::_isReversible' [-Wreorder] + 111 | bool _isReversible; + | ^~~~~~~~~~~~~ +gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] + 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): + | ^~~~~~~~~~~~~ +gainLossModel.h:114:14: warning: 'gainLossModel::_isHGT_with_Q' will be initialized after [-Wreorder] + 114 | bool _isHGT_with_Q; + | ^~~~~~~~~~~~~ +gainLossModel.h:110:15: warning: 'q2pt* gainLossModel::_q2pt' [-Wreorder] + 110 | q2pt *_q2pt; // dont use q2p + | ^~~~~ +gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] + 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): + | ^~~~~~~~~~~~~ +optimizeGainLossModelVV.cpp:258:41: warning: unused variable 'currentlogL' [-Wunused-variable] + 258 | MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); + | ^~~~~~~~~~~ +In file included from mainbb.cpp:31: +../../libs/phylogeny/bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': +../../libs/phylogeny/bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] + 175 | stochasticProcess& _sp; + | ^~~ +../../libs/phylogeny/bestGtrModelParams.h:173:34: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] + 173 | const gammaDistribution* _pProportionDist; + | ^~~~~~~~~~~~~~~~ +../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] + 162 | C_evalGTRParamProportional( const GTRParam param, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +optimizeGainLossModelVV.cpp:76:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] + 76 | MDOUBLE sumPijQij; + | ^~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': gainLoss.cpp:1245:64: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ @@ -1625,12 +1656,6 @@ 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ | ^~~~~~~~~~~~~~~~~~~ | ( ) -In file included from mainbb.h:4, - from mainbb.cpp:1: -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': gainLoss.cpp:1868:25: warning: unused variable 'sumPijQij' [-Wunused-variable] 1868 | MDOUBLE sumPijQij = normalizeQ(sp); @@ -1639,17 +1664,34 @@ gainLoss.cpp:1990:25: warning: unused variable 'sumPijQij' [-Wunused-variable] 1990 | MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); | ^~~~~~~~~ -indelCoder.cpp: In member function 'void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)': -indelCoder.cpp:175:33: warning: 'condition' may be used uninitialized [-Wmaybe-uninitialized] - 175 | while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -indelCoder.cpp:170:22: note: 'condition' was declared here - 170 | bool condition; - | ^~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp +In file included from siteSpecificGL.cpp:24: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from computePosteriorExpectationOfChange.cpp:25: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'double gainLoss::computeDistanceFromRootForRecent(tree&)': gainLoss.cpp:4205:14: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] 4205 | bool isRecentBiggerAncient = true; | ^~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp gainLoss.cpp: In member function 'double gainLoss::computeDistanceNearestOTUforRecent(tree&)': gainLoss.cpp:4283:14: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] 4283 | bool isRecentBiggerAncient = true; @@ -1662,39 +1704,8 @@ 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ | ^~~~~~~~~~~ | ( ) -gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const std::string&)': -gainLossOptions.cpp:2064:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] - 2064 | return returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp:2047:27: note: 'returnType' was declared here - 2047 | optimizationLevel returnType; - | ^~~~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::startSimultePosteriorExpectationOfChange(int, int)': -gainLoss.cpp:4951:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] - 4951 | MDOUBLE sumQii = 1.0; - | ^~~~~~ -gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const std::string&)': -gainLossOptions.cpp:2111:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] - 2111 | return returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp:2098:24: note: 'returnType' was declared here - 2098 | costMatrixType returnType; - | ^~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp In file included from gainLoss.h:35, - from gainLossOptimizer.h:24, - from gainLossOptimizer.cpp:17: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from computePosteriorExpectationOfChange.cpp:25: + from gainLossProject.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] @@ -1705,8 +1716,27 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::startSimultePosteriorExpectationOfChange(int, int)': +gainLoss.cpp:4951:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] + 4951 | MDOUBLE sumQii = 1.0; + | ^~~~~~ +In file included from mainbb.h:4, + from mainbb.cpp:1: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] + 62 | static const string usege_splash_screen() { + | ^~~~~~~~~~~~~~~~~~~ +gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': +gainLossUtils.cpp:312:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] + 312 | return res; + | ^~~ +gainLossUtils.cpp:285:17: note: 'res' was declared here + 285 | MDOUBLE res; + | ^~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp In file included from gainLoss.h:35, - from gainLossProject.cpp:17: + from gainLossOptimizer.h:24, + from gainLossOptimizer.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] @@ -1717,6 +1747,7 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp In file included from gainLossOptimizer.cpp:20: bblLS.h: At global scope: bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] @@ -1821,30 +1852,14 @@ gainLossOptimizer.cpp:623:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] 623 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': -gainLossUtils.cpp:312:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] - 312 | return res; - | ^~~ -gainLossUtils.cpp:285:17: note: 'res' was declared here - 285 | MDOUBLE res; - | ^~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp +indelCoder.cpp: In member function 'void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)': +indelCoder.cpp:175:33: warning: 'condition' may be used uninitialized [-Wmaybe-uninitialized] + 175 | while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +indelCoder.cpp:170:22: note: 'condition' was declared here + 170 | bool condition; + | ^~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp -In file included from gainLoss.h:35, - from computeCountsGL.h:24, - from computeCountsGL.cpp:17: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/iostream:39, from ../../libs/phylogeny/readTree.h:6, from ../../libs/phylogeny/tree.h:7, @@ -1879,6 +1894,8 @@ computePosteriorExpectationOfChange.cpp:215:27: note: 'Down' was declared here 215 | doubleRep resDXY, Down, Up; | ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp In file included from gainLoss.h:35, from rate4siteGL.h:24, from rate4siteGL.cpp:17: @@ -1892,6 +1909,51 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from gainLoss.h:35, + from computeCountsGL.h:24, + from computeCountsGL.cpp:17: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp +gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const std::string&)': +gainLossOptions.cpp:2064:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] + 2064 | return returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp:2047:27: note: 'returnType' was declared here + 2047 | optimizationLevel returnType; + | ^~~~~~~~~~ +rate4siteGL.h: In constructor 'rate4siteGL::rate4siteGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, unObservableData*)': +rate4siteGL.h:59:14: warning: 'rate4siteGL::_tr' will be initialized after [-Wreorder] + 59 | tree _tr; + | ^~~ +rate4siteGL.h:58:28: warning: 'stochasticProcess* rate4siteGL::_sp' [-Wreorder] + 58 | stochasticProcess *_sp; + | ^~~ +rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder] + 24 | rate4siteGL::rate4siteGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, unObservableData* unObservableData_p): + | ^~~~~~~~~~~ +rate4siteGL.cpp: In member function 'void rate4siteGL::printRatesBayes(std::ostream&, const Vdouble&)': +rate4siteGL.cpp:151:13: warning: unused variable 'precisionHigh' [-Wunused-variable] + 151 | int precisionHigh = 5; + | ^~~~~~~~~~~~~ +rate4siteGL.cpp:152:13: warning: unused variable 'precisionLow' [-Wunused-variable] + 152 | int precisionLow = 3; + | ^~~~~~~~~~~~ +gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const std::string&)': +gainLossOptions.cpp:2111:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] + 2111 | return returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp:2098:24: note: 'returnType' was declared here + 2098 | costMatrixType returnType; + | ^~~~~~~~~~ computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, VVdouble&, double, bool)': computeCountsGL.h:104:14: warning: 'computeCountsGL::_tr' will be initialized after [-Wreorder] 104 | tree _tr; @@ -1930,36 +1992,6 @@ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] 33 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp -ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o -ar: creating libindelCoder.a -a - indelCoder.o -a - indelCoderOptions.o -a - indelCoderProject.o -a - indelCoderUtils.o -a - character.o -a - gaps.o -ranlib libindelCoder.a -g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder -rate4siteGL.h: In constructor 'rate4siteGL::rate4siteGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, unObservableData*)': -rate4siteGL.h:59:14: warning: 'rate4siteGL::_tr' will be initialized after [-Wreorder] - 59 | tree _tr; - | ^~~ -rate4siteGL.h:58:28: warning: 'stochasticProcess* rate4siteGL::_sp' [-Wreorder] - 58 | stochasticProcess *_sp; - | ^~~ -rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder] - 24 | rate4siteGL::rate4siteGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, unObservableData* unObservableData_p): - | ^~~~~~~~~~~ -rate4siteGL.cpp: In member function 'void rate4siteGL::printRatesBayes(std::ostream&, const Vdouble&)': -rate4siteGL.cpp:151:13: warning: unused variable 'precisionHigh' [-Wunused-variable] - 151 | int precisionHigh = 5; - | ^~~~~~~~~~~~~ -rate4siteGL.cpp:152:13: warning: unused variable 'precisionLow' [-Wunused-variable] - 152 | int precisionLow = 3; - | ^~~~~~~~~~~~ -make[3]: Leaving directory '/build/fastml-3.11/programs/indelCoder' -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp In file included from gainLoss.h:35, from computeCorrelations.h:25, from computeCorrelations.cpp:17: @@ -1973,9 +2005,16 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +computeCorrelations.cpp: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)': +computeCorrelations.cpp:130:13: warning: unused variable 'numOfbranches' [-Wunused-variable] + 130 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node + | ^~~~~~~~~~~~~ +computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': +computeCorrelations.cpp:408:29: warning: unused variable 'isHigherNminReducedFreqOfHighCorr' [-Wunused-variable] + 408 | int isHigherNminReducedFreqOfHighCorr = false; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:35, - from gainLoss4site.h:24, - from gainLoss4site.cpp:17: + from simulateChangesAlongTree.cpp:20: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] @@ -1986,14 +2025,6 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -computeCorrelations.cpp: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)': -computeCorrelations.cpp:130:13: warning: unused variable 'numOfbranches' [-Wunused-variable] - 130 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node - | ^~~~~~~~~~~~~ -computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': -computeCorrelations.cpp:408:29: warning: unused variable 'isHigherNminReducedFreqOfHighCorr' [-Wunused-variable] - 408 | int isHigherNminReducedFreqOfHighCorr = false; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:348:21: warning: unused variable 'typeIndex' [-Wunused-variable] 348 | int typeIndex = corIndex % _EventTypes.size(); // in case both Spearman and pearson are used | ^~~~~~~~~ @@ -2004,33 +2035,25 @@ computeCorrelations.cpp:569:38: warning: NULL used in arithmetic [-Wpointer-arith] 569 | if(!simCorrelStream==NULL) | ^~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp -gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::string&, unObservableData*, double)': -gainLoss4site.h:68:14: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] - 68 | tree _tr; - | ^~~ -gainLoss4site.h:61:45: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] - 61 | vector > _spVVec; //save stochasticProcess for each category - | ^~~~~~~ -gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] - 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, - | ^~~~~~~~~~~~~ -gainLoss4site.h:79:27: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] - 79 | unObservableData* _unObservableData_p; // - | ^~~~~~~~~~~~~~~~~~~ -gainLoss4site.h:78:17: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] - 78 | MDOUBLE _alphaConf; - | ^~~~~~~~~~ -gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] - 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, - | ^~~~~~~~~~~~~ computeCorrelations.cpp:579:38: warning: NULL used in arithmetic [-Wpointer-arith] 579 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:584:30: warning: NULL used in arithmetic [-Wpointer-arith] 584 | if(!simCorrelStream==NULL) | ^~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp +In file included from gainLoss.h:35, + from gainLoss4site.h:24, + from gainLoss4site.cpp:17: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)': computeCorrelations.cpp:676:37: warning: variable 'prevNumberOfSimulationsInRange' set but not used [-Wunused-but-set-variable] 676 | int prevNumberOfSimulationsInRange = 1; @@ -2066,25 +2089,27 @@ computeCorrelations.cpp:1300:14: warning: variable 'it_siteB' set but not used [-Wunused-but-set-variable] 1300 | it_B it_siteB = it_siteA->second.begin(); | ^~~~~~~~ -mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': -mainbb.cpp:428:108: warning: 'bm' may be used uninitialized [-Wmaybe-uninitialized] - 428 | bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); - | ^ -mainbb.cpp:423:28: note: 'bm' was declared here - 423 | bbAlg::boundMethod bm; - | ^~ -In file included from gainLoss.h:35, - from simulateChangesAlongTree.cpp:20: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::string&, unObservableData*, double)': +gainLoss4site.h:68:14: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] + 68 | tree _tr; + | ^~~ +gainLoss4site.h:61:45: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] + 61 | vector > _spVVec; //save stochasticProcess for each category + | ^~~~~~~ +gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] + 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, + | ^~~~~~~~~~~~~ +gainLoss4site.h:79:27: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] + 79 | unObservableData* _unObservableData_p; // + | ^~~~~~~~~~~~~~~~~~~ +gainLoss4site.h:78:17: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] + 78 | MDOUBLE _alphaConf; + | ^~~~~~~~~~ +gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] + 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, + | ^~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp In file included from gainLoss.h:35, from simulateOnePos.cpp:32: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': @@ -2133,6 +2158,17 @@ simulateOnePos.cpp:202:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] 202 | MDOUBLE sumQii = 1.0; | ^~~~~~ +ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o +ar: creating libindelCoder.a +a - indelCoder.o +a - indelCoderOptions.o +a - indelCoderProject.o +a - indelCoderUtils.o +a - character.o +a - gaps.o +ranlib libindelCoder.a +g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder +make[3]: Leaving directory '/build/fastml-3.11/programs/indelCoder' In file included from bblLS.cpp:17: bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); @@ -2168,24 +2204,13 @@ bblLS.cpp:112:21: warning: NULL used in arithmetic [-Wpointer-arith] 112 | if (curL == NULL) | ^~~~ -ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o -ar: creating libfastml.a -a - fastml.o -a - bbAlg.o -a - bbComputeDownAlg.o -a - bbComputeUpAlg.o -a - bbEvaluateSpecificAV.o -a - bbfindBestAVDynProg.o -a - bbNodeOrderAlg.o -a - bb_options.o -a - bbReport.o -a - computeMarginalReconstruction.o -a - jointNoGamma.o -a - mainbb.o -a - sequenceDataDiff.o -a - suffStatComponentJointNoGamma.o -ranlib libfastml.a -g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml +mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': +mainbb.cpp:428:108: warning: 'bm' may be used uninitialized [-Wmaybe-uninitialized] + 428 | bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); + | ^ +mainbb.cpp:423:28: note: 'bm' was declared here + 423 | bbAlg::boundMethod bm; + | ^~ In file included from sankoffReconstructGL.cpp:17: sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)': sankoffReconstructGL.h:85:16: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] @@ -2206,6 +2231,24 @@ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): | ^~~~~~~~~~~~~~~~~~~~ +ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o +ar: creating libfastml.a +a - fastml.o +a - bbAlg.o +a - bbComputeDownAlg.o +a - bbComputeUpAlg.o +a - bbEvaluateSpecificAV.o +a - bbfindBestAVDynProg.o +a - bbNodeOrderAlg.o +a - bb_options.o +a - bbReport.o +a - computeMarginalReconstruction.o +a - jointNoGamma.o +a - mainbb.o +a - sequenceDataDiff.o +a - suffStatComponentJointNoGamma.o +ranlib libfastml.a +g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': gainLossOptimizer.cpp:833:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] 833 | return res; @@ -2365,13 +2408,6 @@ gainLoss.cpp:806:23: note: 'rateDist' was declared here 806 | distribution* rateDist; | ^~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::startStochasticProcessVec()': -gainLoss.cpp:1127:46: warning: 'rateDist' may be used uninitialized [-Wmaybe-uninitialized] - 1127 | if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted - | ^~~~~~~~ -gainLoss.cpp:1105:39: note: 'rateDist' was declared here - 1105 | distribution* rateDist; - | ^~~~~~~~ computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': computeCorrelations.cpp:505:33: warning: 'expextedFreq' may be used uninitialized [-Wmaybe-uninitialized] 505 | if(freqOfHighCorr>expextedFreq && freqOfHighCorr doubleRep.out.tmp -diff doubleRep.out.tmp doubleRep.out.standard ./split_test > split_test.out.tmp diff split_test.out.tmp split_test.out.standard +./doubleRep > doubleRep.out.tmp +diff doubleRep.out.tmp doubleRep.out.standard ./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp -./splitMap_test > splitMap_test.out.tmp diff readTreeWithComments.out.tmp readTreeWithComments.out.standard +./splitMap_test > splitMap_test.out.tmp diff splitMap_test.out.tmp splitMap_test.out.standard -./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp -diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard -./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp -diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard -./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp ./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp -diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard ./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard +./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp +diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard +./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp +diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard +./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp +diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard make[4]: Leaving directory '/build/fastml-3.11/libs/phylogeny/tests' make[3]: Leaving directory '/build/fastml-3.11/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.11/libs' @@ -2480,7 +2523,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/fastml/ - make -j15 install DESTDIR=/build/fastml-3.11/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j16 install DESTDIR=/build/fastml-3.11/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/fastml-3.11' cd libs;make all make[2]: Entering directory '/build/fastml-3.11/libs' @@ -2493,16 +2536,16 @@ make[2]: Entering directory '/build/fastml-3.11/programs' cd fastml && make install cd gainLoss && make install -cd indelCoder && make install make[3]: Entering directory '/build/fastml-3.11/programs/fastml' mkdir -p ../../bin +cd indelCoder && make install cp fastml ../../bin/fastml make[3]: Entering directory '/build/fastml-3.11/programs/gainLoss' mkdir -p ../../bin make[3]: Entering directory '/build/fastml-3.11/programs/indelCoder' mkdir -p ../../bin -cp gainLoss ../../bin/gainLoss cp indelCoder ../../bin/indelCoder +cp gainLoss ../../bin/gainLoss make[3]: Leaving directory '/build/fastml-3.11/programs/indelCoder' make[3]: Leaving directory '/build/fastml-3.11/programs/fastml' make[3]: Leaving directory '/build/fastml-3.11/programs/gainLoss' @@ -2535,12 +2578,14 @@ 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/3628022/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3628022/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/631674 and its subdirectories -I: Current time: Mon May 15 07:21:27 -12 2023 -I: pbuilder-time-stamp: 1684178487 +I: removing directory /srv/workspace/pbuilder/3628022 and its subdirectories +I: Current time: Mon Jun 17 15:54:06 +14 2024 +I: pbuilder-time-stamp: 1718589246