Diff of the two buildlogs: -- --- b1/build.log 2021-03-30 21:56:50.324508264 +0000 +++ b2/build.log 2021-03-30 22:00:01.845008348 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 2 16:17:20 -12 2022 -I: pbuilder-time-stamp: 1651551440 +I: Current time: Wed Mar 31 11:56:52 +14 2021 +I: pbuilder-time-stamp: 1617141412 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Wed Jul 11 07:30:13 2018 -12 +gpgv: Signature made Thu Jul 12 09:30:13 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -36,136 +36,170 @@ dpkg-source: info: applying g++-6.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/54242/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/11389/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/11389/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/11389/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=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(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=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='516c9e8ed33b4e758625bb61a7fee655' - 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='54242' - PS1='# ' - PS2='> ' + INVOCATION_ID=53ab8ee05ccd4148b15192a8b59b98af + 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=11389 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.4eXPlHRDOc/pbuilderrc_cBEV --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4eXPlHRDOc/b1 --logfile b1/build.log fastml_3.1-4.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://85.184.249.68:3128' + 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/tmp.4eXPlHRDOc/pbuilderrc_vTkQ --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4eXPlHRDOc/b2 --logfile b2/build.log fastml_3.1-4.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 5.10.0-0.bpo.3-amd64 #1 SMP Debian 5.10.13-1~bpo10+1 (2021-02-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Apr 23 02:46 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/54242/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Mar 31 11:57 sh -> bash + lrwxrwxrwx 1 root root 4 Mar 21 22:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/11389/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -234,7 +268,7 @@ Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] -Fetched 19.0 MB in 0s (59.3 MB/s) +Fetched 19.0 MB in 0s (48.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -389,7 +423,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/fastml-3.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/fastml-3.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.1-4 dpkg-buildpackage: info: source distribution unstable @@ -401,7 +435,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/fastml-3.1' dh_auto_clean - make -j16 clean + make -j15 clean make[2]: Entering directory '/build/fastml-3.1' cd libs;make clean cd programs;make clean @@ -411,18 +445,18 @@ cd fastml && make clean cd gainLoss && make clean cd indelCoder && make clean -make[4]: Entering directory '/build/fastml-3.1/programs/fastml' -rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o -make[4]: Entering directory '/build/fastml-3.1/programs/indelCoder' -rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Entering directory '/build/fastml-3.1/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o -make[4]: Leaving directory '/build/fastml-3.1/programs/fastml' +make[4]: Entering directory '/build/fastml-3.1/programs/indelCoder' +rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o +make[4]: Entering directory '/build/fastml-3.1/programs/fastml' +rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Entering directory '/build/fastml-3.1/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o -make[4]: Leaving directory '/build/fastml-3.1/programs/indelCoder' make[4]: Leaving directory '/build/fastml-3.1/libs/phylogeny' make[3]: Leaving directory '/build/fastml-3.1/libs' +make[4]: Leaving directory '/build/fastml-3.1/programs/indelCoder' +make[4]: Leaving directory '/build/fastml-3.1/programs/fastml' make[4]: Leaving directory '/build/fastml-3.1/programs/gainLoss' make[3]: Leaving directory '/build/fastml-3.1/programs' make[2]: Leaving directory '/build/fastml-3.1' @@ -438,7 +472,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j16 "INSTALL=install --strip-program=true" + make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/fastml-3.1' cd libs;make all make[2]: Entering directory '/build/fastml-3.1/libs' @@ -463,7 +497,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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:184:10: warning: variable 'ax' set but not used [-Wunused-but-set-variable] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha @@ -478,6 +511,7 @@ bestAlpha.cpp:371:10: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] MDOUBLE oldA=0; ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp @@ -493,7 +527,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp In file included from computeSubstitutionCounts.cpp:1: computeSubstitutionCounts.h: In constructor 'computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer&, const tree&, multipleStochasticProcess*, std::__cxx11::string&, VVVdouble&, int, double, bool)': computeSubstitutionCounts.h:57:12: warning: 'computeSubstitutionCounts::_LpostPerSpPerCat' will be initialized after [-Wreorder] @@ -515,6 +548,7 @@ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 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-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp @@ -529,7 +563,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.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:29:12: warning: 'fromCountTableComponentToDistancePropEB::_nodeID' will be initialized after [-Wreorder] @@ -541,6 +574,7 @@ fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp @@ -553,8 +587,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)': goldmanYangModel.cpp:8:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV): @@ -563,6 +595,8 @@ goldmanYangModel.cpp:18:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): ^~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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:274:18: required from here @@ -578,6 +612,8 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] //* for (i=1;i&, VVdouble&, njConstraint&)': -nj.cpp:122:13: warning: 'minCol' may be used uninitialized in this function [-Wmaybe-uninitialized] - int minRaw,minCol; - ^~~~~~ -nj.cpp:133:36: warning: 'minRaw' may be used uninitialized in this function [-Wmaybe-uninitialized] - UpdateDistanceTableAndCurrentNodes(currentNodes,distanceTable,nodeI,nodeJ,theNewNode,minRaw,minCol); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequenceContainer.cpp: In member function 'void sequenceContainer::removeGapPositions()': sequenceContainer.cpp:187:7: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] bool gapCol; @@ -626,10 +650,22 @@ sequenceContainer.cpp:467:12: warning: unused variable 'len' [-Wunused-variable] const int len = _seqDataVec[0].seqLen(); ^~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.cpp sequence.cpp: In constructor 'sequence::sequence(const sequence&, const alphabet*)': sequence.cpp:76:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses] || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcess.o stochasticProcess.cpp +nj.cpp: In member function 'void NJalg::NJiterate(tree&, std::vector&, VVdouble&, njConstraint&)': +nj.cpp:122:13: warning: 'minCol' may be used uninitialized in this function [-Wmaybe-uninitialized] + int minRaw,minCol; + ^~~~~~ +nj.cpp:133:36: warning: 'minRaw' may be used uninitialized in this function [-Wmaybe-uninitialized] + UpdateDistanceTableAndCurrentNodes(currentNodes,distanceTable,nodeI,nodeJ,theNewNode,minRaw,minCol); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp nj.cpp: In member function 'void NJalg::NJiterate(tree&, std::vector&, VVdouble&)': nj.cpp:100:41: warning: 'minCol' may be used uninitialized in this function [-Wmaybe-uninitialized] tree::nodeP nodeJ = currentNodes[minCol]; @@ -637,16 +673,12 @@ nj.cpp:99:41: warning: 'minRaw' may be used uninitialized in this function [-Wmaybe-uninitialized] tree::nodeP nodeI = currentNodes[minRaw]; ^ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp tree.cpp: In constructor 'tree::tree(const string&)': tree.cpp:180:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (in.is_open()) @@ -654,6 +686,12 @@ tree.cpp:182:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' create_names_to_internal_nodes(); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp treeUtil.cpp: In function 'std::vector getNexusTreesFromFile(const string&)': treeUtil.cpp:371:25: warning: variable 'itStrStart' set but not used [-Wunused-but-set-variable] string::const_iterator itStrStart = it->begin(); @@ -661,10 +699,6 @@ treeUtil.cpp:372:25: warning: variable 'itStrEnd' set but not used [-Wunused-but-set-variable] string::const_iterator itStrEnd = it->end(); ^~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp @@ -692,6 +726,9 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistribution.o betaDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp In file included from betaDistribution.cpp:3: betaDistribution.h: In copy constructor 'betaDistribution::betaDistribution(const betaDistribution&)': betaDistribution.h:54:18: warning: 'betaDistribution::_boundary' will be initialized after [-Wreorder] @@ -703,9 +740,6 @@ betaDistribution.cpp:23:1: warning: when initialized here [-Wreorder] betaDistribution::betaDistribution(const betaDistribution& other) : ^~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp @@ -744,11 +778,6 @@ computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp -seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)': -seqeuncesFilter.cpp:141:18: warning: unused variable 'pAlph' [-Wunused-variable] - const alphabet* pAlph = sc.getAlphabet(); - ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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:123:12: warning: variable 'Exp_Rk' set but not used [-Wunused-but-set-variable] MDOUBLE Exp_Rk, Exp_LogRk, sum; @@ -772,7 +801,21 @@ suffStatGammaMixture.cpp:216:10: warning: variable 'res2' set but not used [-Wunused-but-set-variable] MDOUBLE res2 = 0.0; ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp +seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)': +seqeuncesFilter.cpp:141:18: warning: unused variable 'pAlph' [-Wunused-variable] + const alphabet* pAlph = sc.getAlphabet(); + ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp +In file included from GamMixtureOptimizer.cpp:3: +optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': +optGammaMixtureEM.h:76:11: warning: unused variable 'res1' [-Wunused-variable] + 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:87:11: warning: unused variable 'debugRes' [-Wunused-variable] + 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))); + ^~~~~~~~ mixtureDistribution.cpp: In member function 'virtual const double mixtureDistribution::rates(int) const': mixtureDistribution.cpp:210:6: warning: 'componentNum' may be used uninitialized in this function [-Wmaybe-uninitialized] int componentNum, categoryInComponent, totalCat = 0; @@ -792,7 +835,7 @@ mixtureDistribution.cpp:228:20: note: 'categoryInComponent' was declared here int componentNum, categoryInComponent, totalCat = 0; ^~~~~~~~~~~~~~~~~~~ -In file included from GamMixtureOptimizer.cpp:3: +In file included from optGammaMixtureEM.cpp:1: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': optGammaMixtureEM.h:76:11: warning: unused variable 'res1' [-Wunused-variable] MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); @@ -801,6 +844,8 @@ optGammaMixtureEM.h:87:11: warning: unused variable 'debugRes' [-Wunused-variable] 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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp In file included from seqeuncesFilter.h:6, from seqeuncesFilter.cpp:1: sequenceContainer.h: In static member function 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const string&, std::__cxx11::string)': @@ -810,17 +855,6 @@ seqeuncesFilter.cpp:165:6: note: 'refID' was declared here int refID; ^~~~~ -In file included from optGammaMixtureEM.cpp:1: -optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': -optGammaMixtureEM.h:76:11: warning: unused variable 'res1' [-Wunused-variable] - 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:87:11: warning: unused variable 'debugRes' [-Wunused-variable] - 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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp @@ -1056,12 +1090,12 @@ make[2]: Entering directory '/build/fastml-3.1/programs' cd fastml && make all cd gainLoss && make all -cd indelCoder && make all make[3]: Entering directory '/build/fastml-3.1/programs/fastml' making depend +cd indelCoder && make all make[3]: Entering directory '/build/fastml-3.1/programs/gainLoss' -make[3]: Entering directory '/build/fastml-3.1/programs/indelCoder' making depend +make[3]: Entering directory '/build/fastml-3.1/programs/indelCoder' making depend g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp @@ -1069,20 +1103,22 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o character.o character.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp +character.cpp: In member function 'int character::getLongestGapStIndex()': +character.cpp:28:9: warning: 'longestGapStIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] + return longestGapStIndex; + ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': indelCoder.cpp:422:6: warning: unused variable 'gapNum' [-Wunused-variable] int gapNum = 1; ^~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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 indelCoder.cpp: In member function 'void indelCoder::printIndelSummary()': indelCoder.cpp:587:7: warning: unused variable 'isSIC' [-Wunused-variable] bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; @@ -1090,15 +1126,14 @@ indelCoder.cpp:597:6: warning: unused variable 'seqLeng' [-Wunused-variable] int seqLeng = _sc.seqLen(); ^~~~~~~ -character.cpp: In member function 'int character::getLongestGapStIndex()': -character.cpp:28:9: warning: 'longestGapStIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] - return longestGapStIndex; - ^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp character.cpp: In member function 'void character::checkForTriangleInequality(int, int)': character.cpp:6:63: warning: 'longestGapStIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][longestGapStIndex]){ ^ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp In file included from bbAlg.h:8, from fastml.cpp:254: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': @@ -1111,8 +1146,6 @@ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp In file included from bbReport.cpp:1: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] @@ -1124,6 +1157,7 @@ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp In file included from bbEvaluateSpecificAV.cpp:1: bbEvaluateSpecificAV.h: In constructor 'bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&)': bbEvaluateSpecificAV.h:34:27: warning: 'bbEvaluateSpecificAV::_sc' will be initialized after [-Wreorder] @@ -1139,6 +1173,61 @@ bbEvaluateSpecificAV.cpp:65:12: warning: unused variable 'rate' [-Wunused-variable] MDOUBLE rate = _sp.rates(categor); // the r. ^~~~ +In file included from bbAlg.h:8, + from bbAlg.cpp:1: +bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': +bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] + const string& _reportFileName; + ^~~~~~~~~~~~~~~ +bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] + const int _minNumOfNodesToVisit; + ^~~~~~~~~~~~~~~~~~~~~ +bbReport.h:10:11: warning: when initialized here [-Wreorder] + explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) + ^~~~~~~~~~~~~~~~~ +In file included from bbAlg.cpp:1: +bbAlg.h: In constructor 'bbAlg::bbAlg(const tree&, std::vector&, const sequenceContainer&, bbAlg::boundMethod, const string&, double, const distribution*)': +bbAlg.h:61:16: warning: 'bbAlg::_reportFileName' will be initialized after [-Wreorder] + const string& _reportFileName; + ^~~~~~~~~~~~~~~ +bbAlg.h:60:20: warning: 'BandBReportAllPos bbAlg::BandBReportAllPos1' [-Wreorder] + BandBReportAllPos BandBReportAllPos1; // report for all positions. + ^~~~~~~~~~~~~~~~~~ +bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] + bbAlg::bbAlg(const tree& et, + ^~~~~ +In file included from bbAlg.cpp:1: +bbAlg.h:60:20: warning: 'bbAlg::BandBReportAllPos1' will be initialized after [-Wreorder] + BandBReportAllPos BandBReportAllPos1; // report for all positions. + ^~~~~~~~~~~~~~~~~~ +bbAlg.h:29:14: warning: 'const tree& bbAlg::_et' [-Wreorder] + const tree& _et; + ^~~ +bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] + bbAlg::bbAlg(const tree& et, + ^~~~~ +In file included from bbEvaluateSpecificAV.h:4, + from bbEvaluateSpecificAV.cpp:1: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] + static const string usege_splash_screen() { + ^~~~~~~~~~~~~~~~~~~ +bbReport.h: In constructor 'BandBReport::BandBReport(const string&, int, int)': +bbReport.h:53:16: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder] + const string& _reportFileName; + ^~~~~~~~~~~~~~~ +bbReport.h:51:12: warning: 'const int BandBReport::_position' [-Wreorder] + const int _position; + ^~~~~~~~~ +bbReport.cpp:10:1: warning: when initialized here [-Wreorder] + BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : + ^~~~~~~~~~~ +In file included from mainbb.h:4, + from fastml.cpp:1: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] + static const string usege_splash_screen() { + ^~~~~~~~~~~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h: In constructor 'bb_options::bb_options(int&, char**)': bb_options.h:49:9: warning: 'bb_options::reportFile' will be initialized after [-Wreorder] @@ -1220,35 +1309,13 @@ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^~~~~~~~~~ -In file included from bbfindBestAVDynProg.h:5, - from bbfindBestAVDynProg.cpp:1: -bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] - static const string usege_splash_screen() { - ^~~~~~~~~~~~~~~~~~~ -In file included from mainbb.h:4, - from fastml.cpp:1: -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] - static const string usege_splash_screen() { - ^~~~~~~~~~~~~~~~~~~ -In file included from bb_options.cpp:2: -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] - static const string usege_splash_screen() { - ^~~~~~~~~~~~~~~~~~~ -In file included from bbAlg.h:8, - from bbAlg.cpp:1: -bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': -bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] - const string& _reportFileName; - ^~~~~~~~~~~~~~~ -bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] - const int _minNumOfNodesToVisit; - ^~~~~~~~~~~~~~~~~~~~~ -bbReport.h:10:11: warning: when initialized here [-Wreorder] - explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) - ^~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp +computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': +computeMarginalReconstruction.cpp:67:11: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] + MDOUBLE likelihoodOfPos = 0; + ^~~~~~~~~~~~~~~ +computeMarginalReconstruction.cpp:45:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] + MDOUBLE totalLikelihoodOfReconstruction = 0; + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bbNodeOrderAlg.cpp:1: bbNodeOrderAlg.h: In constructor 'bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)': bbNodeOrderAlg.h:33:27: warning: 'bbNodeOrderAlg::_sc' will be initialized after [-Wreorder] @@ -1260,50 +1327,11 @@ bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, ^~~~~~~~~~~~~~ -bbReport.h: In constructor 'BandBReport::BandBReport(const string&, int, int)': -bbReport.h:53:16: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder] - const string& _reportFileName; - ^~~~~~~~~~~~~~~ -bbReport.h:51:12: warning: 'const int BandBReport::_position' [-Wreorder] - const int _position; - ^~~~~~~~~ -bbReport.cpp:10:1: warning: when initialized here [-Wreorder] - BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : - ^~~~~~~~~~~ -In file included from bbEvaluateSpecificAV.h:4, - from bbEvaluateSpecificAV.cpp:1: +In file included from bb_options.cpp:2: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ -In file included from bbAlg.cpp:1: -bbAlg.h: In constructor 'bbAlg::bbAlg(const tree&, std::vector&, const sequenceContainer&, bbAlg::boundMethod, const string&, double, const distribution*)': -bbAlg.h:61:16: warning: 'bbAlg::_reportFileName' will be initialized after [-Wreorder] - const string& _reportFileName; - ^~~~~~~~~~~~~~~ -bbAlg.h:60:20: warning: 'BandBReportAllPos bbAlg::BandBReportAllPos1' [-Wreorder] - BandBReportAllPos BandBReportAllPos1; // report for all positions. - ^~~~~~~~~~~~~~~~~~ -bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] - bbAlg::bbAlg(const tree& et, - ^~~~~ -In file included from bbAlg.cpp:1: -bbAlg.h:60:20: warning: 'bbAlg::BandBReportAllPos1' will be initialized after [-Wreorder] - BandBReportAllPos BandBReportAllPos1; // report for all positions. - ^~~~~~~~~~~~~~~~~~ -bbAlg.h:29:14: warning: 'const tree& bbAlg::_et' [-Wreorder] - const tree& _et; - ^~~ -bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] - bbAlg::bbAlg(const tree& et, - ^~~~~ -computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': -computeMarginalReconstruction.cpp:67:11: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] - MDOUBLE likelihoodOfPos = 0; - ^~~~~~~~~~~~~~~ -computeMarginalReconstruction.cpp:45:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] - MDOUBLE totalLikelihoodOfReconstruction = 0; - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': jointNoGamma.cpp:23:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] MDOUBLE totalLikelihoodOfReconstruction = 0; @@ -1313,13 +1341,27 @@ MDOUBLE maxL = VERYSMALL; ^~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp +In file included from bbfindBestAVDynProg.h:5, + from bbfindBestAVDynProg.cpp:1: +bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] + static const string usege_splash_screen() { + ^~~~~~~~~~~~~~~~~~~ +In file included from bbNodeOrderAlg.h:5, + from bbAlg.h:5, + from bbAlg.cpp:1: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] + static const string usege_splash_screen() { + ^~~~~~~~~~~~~~~~~~~ In file included from bbNodeOrderAlg.h:5, from bbNodeOrderAlg.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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-3.1=. -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 bbAlg.h:8, from mainbb.cpp:5: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': @@ -1332,15 +1374,7 @@ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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 bbNodeOrderAlg.h:5, - from bbAlg.h:5, - from bbAlg.cpp:1: -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] - static const string usege_splash_screen() { - ^~~~~~~~~~~~~~~~~~~ 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:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] @@ -1354,27 +1388,6 @@ ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp -In file included from gainLossUtils.cpp:19: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - MDOUBLE _loss; // _Q[1][0] - ^~~~~ -gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] - :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - ^ -gainLossModel.h:127:11: warning: when initialized here [-Wreorder] - explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossUtils.cpp: In function 'void printTreeWithValuesAsBP(std::ostream&, tree::TreeNode* const&, Vstring, VVVdouble*, bool)': -gainLossUtils.cpp:72:5: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] - if(probs) - ^ -gainLossUtils.cpp:88:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] - if(probs) - ^ In file included from optimizeGainLossModel.h:27, from optimizeGainLossModel.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': @@ -1398,19 +1411,24 @@ optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, ^~~~~~~~~~~~~~~~~~~~~ -gainLossUtils.cpp: In function 'void updateGainBeta(double, std::vector >&, distribution*, distribution*, bool)': -gainLossUtils.cpp:481:10: warning: variable 'normFactor' set but not used [-Wunused-but-set-variable] - MDOUBLE normFactor; - ^~~~~~~~~~ -gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': -gainLossUtils.cpp:788:10: warning: unused variable 'scale' [-Wunused-variable] - MDOUBLE scale; +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 gainLoss.h:35, + from gainLoss.cpp:20: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + MDOUBLE _loss; // _Q[1][0] ^~~~~ +gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] + :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + ^ +gainLossModel.h:127:11: warning: when initialized here [-Wreorder] + explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + ^~~~~~~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.cpp:85:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] MDOUBLE sumPijQij; ^~~~~~~~~ -In file included from gainLoss.h:35, - from gainLoss.cpp:20: +In file included from gainLossUtils.cpp:19: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] @@ -1421,12 +1439,13 @@ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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 mainbb.h:4, - from mainbb.cpp:1: -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] - static const string usege_splash_screen() { - ^~~~~~~~~~~~~~~~~~~ +gainLossUtils.cpp: In function 'void printTreeWithValuesAsBP(std::ostream&, tree::TreeNode* const&, Vstring, VVVdouble*, bool)': +gainLossUtils.cpp:72:5: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + if(probs) + ^ +gainLossUtils.cpp:88:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + if(probs) + ^ In file included from gainLoss.cpp:41: bblLS.h: At global scope: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] @@ -1486,7 +1505,34 @@ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^~~~~~~~ -In file included from siteSpecificGL.cpp:24: +gainLossUtils.cpp: In function 'void updateGainBeta(double, std::vector >&, distribution*, distribution*, bool)': +gainLossUtils.cpp:481:10: warning: variable 'normFactor' set but not used [-Wunused-but-set-variable] + MDOUBLE normFactor; + ^~~~~~~~~~ +gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': +gainLossUtils.cpp:788:10: warning: unused variable 'scale' [-Wunused-variable] + MDOUBLE scale; + ^~~~~ +In file included from mainbb.h:4, + from mainbb.cpp:1: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] + static const string usege_splash_screen() { + ^~~~~~~~~~~~~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)': +gainLoss.cpp:604:7: warning: unused variable 'missigDataChar' [-Wunused-variable] + char missigDataChar = -2; + ^~~~~~~~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': +gainLoss.cpp:1245:57: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] + if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ + ^~ +gainLoss.cpp:1245:38: note: add parentheses around left hand side expression to silence this warning + if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ + ^~~~~~~~~~~~~~~~~~~ + ( ) +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:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] @@ -1497,10 +1543,37 @@ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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::removePositionsWithHighPercentOfMissingData(double)': -gainLoss.cpp:604:7: warning: unused variable 'missigDataChar' [-Wunused-variable] - char missigDataChar = -2; - ^~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp +In file included from optimizeGainLossModelVV.cpp:17: +optimizeGainLossModelVV.h: In constructor 'optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)': +optimizeGainLossModelVV.h:82:11: warning: 'optimizeGainLossModelVV::_weightsUniqPatterns' will be initialized after [-Wreorder] + Vdouble* _weightsUniqPatterns; + ^~~~~~~~~~~~~~~~~~~~ +optimizeGainLossModelVV.h:81:20: warning: 'unObservableData* optimizeGainLossModelVV::_unObservableData_p' [-Wreorder] + unObservableData* _unObservableData_p; + ^~~~~~~~~~~~~~~~~~~ +optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] + optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, + ^~~~~~~~~~~~~~~~~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': +gainLoss.cpp:1868:11: warning: unused variable 'sumPijQij' [-Wunused-variable] + MDOUBLE sumPijQij = normalizeQ(sp); + ^~~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': +gainLoss.cpp:1990:11: warning: unused variable 'sumPijQij' [-Wunused-variable] + MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); + ^~~~~~~~~ +optimizeGainLossModelVV.cpp:258:13: warning: unused variable 'currentlogL' [-Wunused-variable] + MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); + ^~~~~~~~~~~ +optimizeGainLossModelVV.cpp:76:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] + MDOUBLE sumPijQij; + ^~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp +gainLoss.cpp: In member function 'double gainLoss::computeDistanceFromRootForRecent(tree&)': +gainLoss.cpp:4205:7: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] + bool isRecentBiggerAncient = true; + ^~~~~~~~~~~~~~~~~~~~~ In file included from gainLossModel.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] @@ -1532,6 +1605,10 @@ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): ^~~~~~~~~~~~~ +gainLoss.cpp: In member function 'double gainLoss::computeDistanceNearestOTUforRecent(tree&)': +gainLoss.cpp:4283:7: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] + bool isRecentBiggerAncient = true; + ^~~~~~~~~~~~~~~~~~~~~ In file included from gainLossModel.cpp:17: gainLossModel.h:114:7: warning: 'gainLossModel::_isHGT_with_Q' will be initialized after [-Wreorder] bool _isHGT_with_Q; @@ -1542,25 +1619,31 @@ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): ^~~~~~~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': -gainLoss.cpp:1245:57: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] - if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ - ^~ -gainLoss.cpp:1245:38: note: add parentheses around left hand side expression to silence this warning - if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ - ^~~~~~~~~~~~~~~~~~~ - ( ) -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp -gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': -gainLoss.cpp:1868:11: warning: unused variable 'sumPijQij' [-Wunused-variable] - MDOUBLE sumPijQij = normalizeQ(sp); - ^~~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': -gainLoss.cpp:1990:11: warning: unused variable 'sumPijQij' [-Wunused-variable] - MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); - ^~~~~~~~~ -In file included from gainLoss.h:35, - from gainLossProject.cpp:17: +gainLoss.cpp: In member function 'void gainLoss::multipleAllBranchesByFactorAtStart(double)': +gainLoss.cpp:4382:19: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] + if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ + ^ +gainLoss.cpp:4382:7: note: add parentheses around left hand side expression to silence this warning + if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ + ^~~~~~~~~~~ + ( ) +gainLoss.cpp: In member function 'void gainLoss::startSimultePosteriorExpectationOfChange(int, int)': +gainLoss.cpp:4951:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] + MDOUBLE sumQii = 1.0; + ^~~~~~ +gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const string&)': +gainLossOptions.cpp:2064:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] + return returnType; + ^~~~~~~~~~ +gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const string&)': +gainLossOptions.cpp:2111:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] + return returnType; + ^~~~~~~~~~ +indelCoder.cpp: In member function 'void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)': +indelCoder.cpp:175:19: warning: 'condition' may be used uninitialized in this function [-Wmaybe-uninitialized] + while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ + ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from computePosteriorExpectationOfChange.cpp:25: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] @@ -1571,7 +1654,7 @@ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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: +In file included from siteSpecificGL.cpp:24: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] @@ -1582,8 +1665,8 @@ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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 optimizeGainLossModelVV.h:27, - from optimizeGainLossModelVV.cpp:17: +In file included from gainLoss.h:35, + from gainLossProject.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] @@ -1594,48 +1677,6 @@ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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:4205:7: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] - bool isRecentBiggerAncient = true; - ^~~~~~~~~~~~~~~~~~~~~ -gainLoss.cpp: In member function 'double gainLoss::computeDistanceNearestOTUforRecent(tree&)': -gainLoss.cpp:4283:7: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] - bool isRecentBiggerAncient = true; - ^~~~~~~~~~~~~~~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::multipleAllBranchesByFactorAtStart(double)': -gainLoss.cpp:4382:19: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] - if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ - ^ -gainLoss.cpp:4382:7: note: add parentheses around left hand side expression to silence this warning - if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ - ^~~~~~~~~~~ - ( ) -In file included from optimizeGainLossModelVV.cpp:17: -optimizeGainLossModelVV.h: In constructor 'optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)': -optimizeGainLossModelVV.h:82:11: warning: 'optimizeGainLossModelVV::_weightsUniqPatterns' will be initialized after [-Wreorder] - Vdouble* _weightsUniqPatterns; - ^~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModelVV.h:81:20: warning: 'unObservableData* optimizeGainLossModelVV::_unObservableData_p' [-Wreorder] - unObservableData* _unObservableData_p; - ^~~~~~~~~~~~~~~~~~~ -optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] - optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, - ^~~~~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModelVV.cpp:258:13: warning: unused variable 'currentlogL' [-Wunused-variable] - MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); - ^~~~~~~~~~~ -optimizeGainLossModelVV.cpp:76:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] - MDOUBLE sumPijQij; - ^~~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::startSimultePosteriorExpectationOfChange(int, int)': -gainLoss.cpp:4951:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] - MDOUBLE sumQii = 1.0; - ^~~~~~ -indelCoder.cpp: In member function 'void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)': -indelCoder.cpp:175:19: warning: 'condition' may be used uninitialized in this function [-Wmaybe-uninitialized] - while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ - ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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: @@ -1649,10 +1690,8 @@ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': -gainLossUtils.cpp:312:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] - return res; - ^~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 gainLossOptimizer.cpp:20: bblLS.h: At global scope: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] @@ -1743,15 +1782,14 @@ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, ^~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengths(int)': gainLossOptimizer.cpp:498:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp gainLossOptimizer.cpp:543:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp gainLossOptimizer.cpp:487:10: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1765,40 +1803,13 @@ gainLossOptimizer.cpp:623:10: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': +gainLossUtils.cpp:312:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] + return res; + ^~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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-3.1=. -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 rate4siteGL.h:24, - from rate4siteGL.cpp:17: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - MDOUBLE _loss; // _Q[1][0] - ^~~~~ -gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] - :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - ^ -gainLossModel.h:127:11: warning: when initialized here [-Wreorder] - 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 rate4siteGL.cpp:17: -rate4siteGL.h: In constructor 'rate4siteGL::rate4siteGL(sequenceContainer&, tree&, stochasticProcess*, std::__cxx11::string&, unObservableData*)': -rate4siteGL.h:59:7: warning: 'rate4siteGL::_tr' will be initialized after [-Wreorder] - tree _tr; - ^~~ -rate4siteGL.h:58:21: warning: 'stochasticProcess* rate4siteGL::_sp' [-Wreorder] - stochasticProcess *_sp; - ^~~ -rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder] - 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:151:6: warning: unused variable 'precisionHigh' [-Wunused-variable] - int precisionHigh = 5; - ^~~~~~~~~~~~~ -rate4siteGL.cpp:152:6: warning: unused variable 'precisionLow' [-Wunused-variable] - int precisionLow = 3; - ^~~~~~~~~~~~ -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)': @@ -1812,21 +1823,8 @@ 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 computeCorrelations.h:25, - from computeCorrelations.cpp:17: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - MDOUBLE _loss; // _Q[1][0] - ^~~~~ -gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] - :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - ^ -gainLossModel.h:127:11: warning: when initialized here [-Wreorder] - 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 gainLoss4site.h:24, - from gainLoss4site.cpp:17: + from rate4siteGL.h:24, + from rate4siteGL.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] @@ -1837,8 +1835,7 @@ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ -ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o -ar: creating libindelCoder.a +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 computeCountsGL.cpp:17: computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::__cxx11::string&, VVdouble&, double, bool)': computeCountsGL.h:104:7: warning: 'computeCountsGL::_tr' will be initialized after [-Wreorder] @@ -1881,6 +1878,68 @@ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): ^~~~~~~~~~~~~~~ +In file included from rate4siteGL.cpp:17: +rate4siteGL.h: In constructor 'rate4siteGL::rate4siteGL(sequenceContainer&, tree&, stochasticProcess*, std::__cxx11::string&, unObservableData*)': +rate4siteGL.h:59:7: warning: 'rate4siteGL::_tr' will be initialized after [-Wreorder] + tree _tr; + ^~~ +rate4siteGL.h:58:21: warning: 'stochasticProcess* rate4siteGL::_sp' [-Wreorder] + stochasticProcess *_sp; + ^~~ +rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder] + 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:151:6: warning: unused variable 'precisionHigh' [-Wunused-variable] + int precisionHigh = 5; + ^~~~~~~~~~~~~ +rate4siteGL.cpp:152:6: warning: unused variable 'precisionLow' [-Wunused-variable] + int precisionLow = 3; + ^~~~~~~~~~~~ +mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': +mainbb.cpp:428:101: warning: 'bm' may be used uninitialized in this function [-Wmaybe-uninitialized] + bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); + ^ +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:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + MDOUBLE _loss; // _Q[1][0] + ^~~~~ +gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] + :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + ^ +gainLossModel.h:127:11: warning: when initialized here [-Wreorder] + 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 simulateChangesAlongTree.cpp:20: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + MDOUBLE _loss; // _Q[1][0] + ^~~~~ +gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] + :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + ^ +gainLossModel.h:127:11: warning: when initialized here [-Wreorder] + explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + ^~~~~~~~~~~~~~~~~~~~~~~~~~ +ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o +In file included from gainLoss.h:35, + from computeCorrelations.h:25, + from computeCorrelations.cpp:17: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + MDOUBLE _loss; // _Q[1][0] + ^~~~~ +gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] + :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + ^ +gainLossModel.h:127:11: warning: when initialized here [-Wreorder] + explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + ^~~~~~~~~~~~~~~~~~~~~~~~~~ +ar: creating libindelCoder.a a - indelCoder.o a - indelCoderOptions.o a - indelCoderProject.o @@ -1928,13 +1987,13 @@ computeCorrelations.cpp:569:24: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp computeCorrelations.cpp:579:24: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^~~~ computeCorrelations.cpp:584:23: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp 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:676:9: warning: variable 'prevNumberOfSimulationsInRange' set but not used [-Wunused-but-set-variable] int prevNumberOfSimulationsInRange = 1; @@ -1956,14 +2015,6 @@ if(!numOfSites_A == numOfSites_B){ ^~~~~~~~~~~~~ ( ) -gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const string&)': -gainLossOptions.cpp:2064:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] - return returnType; - ^~~~~~~~~~ -gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const string&)': -gainLossOptions.cpp:2111:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] - return returnType; - ^~~~~~~~~~ computeCorrelations.cpp: In member function 'void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::__cxx11::string*)': computeCorrelations.cpp:1009:7: warning: unused variable 'isPearson' [-Wunused-variable] bool isPearson = false; @@ -1979,11 +2030,12 @@ it_B it_siteB = it_siteA->second.begin(); ^~~~~~~~ make[3]: Leaving directory '/build/fastml-3.1/programs/indelCoder' -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp -mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': -mainbb.cpp:428:101: warning: 'bm' may be used uninitialized in this function [-Wmaybe-uninitialized] - bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); - ^ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp +gainLoss.cpp: In function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': +gainLoss.cpp:2035:44: warning: 'bestLossProbInvariant' may be used uninitialized in this function [-Wmaybe-uninitialized] + if(probInvariant) updateLossProbInvariant(bestLossProbInvariant,lossDist); + ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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)': @@ -1996,18 +2048,10 @@ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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 simulateChangesAlongTree.cpp:20: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - MDOUBLE _loss; // _Q[1][0] - ^~~~~ -gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] - :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - ^ -gainLossModel.h:127:11: warning: when initialized here [-Wreorder] - explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': +gainLossOptimizer.cpp:833:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] + return res; + ^~~ In file included from simulateOnePos.cpp:18: simulateOnePos.h: In constructor 'simulateOnePos::simulateOnePos(std::__cxx11::string, std::ostream*, std::ostream*, int, std::__cxx11::string, double, double, bool, stochasticProcess*, tree*, Vdouble*, Vdouble*)': simulateOnePos.h:72:7: warning: 'simulateOnePos::_simulateNullModel' will be initialized after [-Wreorder] @@ -2046,12 +2090,6 @@ simulateOnePos.cpp:202:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] MDOUBLE sumQii = 1.0; ^~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp -gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': -gainLossOptimizer.cpp:833:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] - return res; - ^~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 bblLS.cpp:17: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); @@ -2087,6 +2125,17 @@ bblLS.cpp:112:14: warning: NULL used in arithmetic [-Wpointer-arith] if (curL == NULL) ^~~~ +In file included from gainLoss.h:35, + from gainLoss.cpp:20: +gainLossModel.h: In function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': +gainLossModel.h:173:14: warning: 'currM2' may be used uninitialized in this function [-Wmaybe-uninitialized] + _Q[1][1] = -_loss; + ^~~~~~ +gainLoss.cpp:1842:10: note: 'currM2' was declared here + MDOUBLE currM2; + ^~~~~~ +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 In file included from sankoffReconstructGL.cpp:17: sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::__cxx11::string&, double, double)': sankoffReconstructGL.h:85:9: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] @@ -2108,8 +2157,6 @@ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 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 @@ -2126,20 +2173,10 @@ a - suffStatComponentJointNoGamma.o ranlib libfastml.a g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny fastml.o libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml -gainLoss.cpp: In function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': -gainLoss.cpp:2035:44: warning: 'bestLossProbInvariant' may be used uninitialized in this function [-Wmaybe-uninitialized] - if(probInvariant) updateLossProbInvariant(bestLossProbInvariant,lossDist); - ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[3]: Leaving directory '/build/fastml-3.1/programs/fastml' -In file included from gainLoss.h:35, - from gainLoss.cpp:20: -gainLossModel.h: In function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': -gainLossModel.h:173:14: warning: 'currM2' may be used uninitialized in this function [-Wmaybe-uninitialized] - _Q[1][1] = -_loss; - ^~~~~~ -gainLoss.cpp:1842:10: note: 'currM2' was declared here - MDOUBLE currM2; - ^~~~~~ +gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const string&)': +gainLossOptions.cpp:2419:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] + return returnType; + ^~~~~~~~~~ In file included from gainLoss.h:35, from gainLoss.cpp:20: gainLossModel.h: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': @@ -2153,23 +2190,20 @@ gainLoss.cpp:2035:44: warning: 'bestLossProbInvariant' may be used uninitialized in this function [-Wmaybe-uninitialized] if(probInvariant) updateLossProbInvariant(bestLossProbInvariant,lossDist); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const string&)': -gainLossOptions.cpp:2419:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] - return returnType; - ^~~~~~~~~~ +make[3]: Leaving directory '/build/fastml-3.1/programs/fastml' gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()': gainLoss.cpp:3980:52: warning: 'AlphaLoss' may be used uninitialized in this function [-Wmaybe-uninitialized] gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); ~~~~~~~~~~^~~~~~~~~~~ gainLoss.cpp:3980:52: warning: 'AlphaGain' may be used uninitialized in this function [-Wmaybe-uninitialized] -computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': -computeCorrelations.cpp:505:5: warning: 'expextedFreq' may be used uninitialized in this function [-Wmaybe-uninitialized] - if(freqOfHighCorr>expextedFreq && freqOfHighCorrexpextedFreq && freqOfHighCorrreadTreeWithComments.out.tmp diff readTreeWithComments.out.tmp readTreeWithComments.out.standard -./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp -diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard -./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp -diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard ./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard ./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard +./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp +diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard +./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp +diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard make[4]: Leaving directory '/build/fastml-3.1/libs/phylogeny/tests' @@ -2272,7 +2306,7 @@ dh_testroot dh_prep dh_auto_install - make -j16 install DESTDIR=/build/fastml-3.1/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j15 install DESTDIR=/build/fastml-3.1/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/fastml-3.1' cd libs;make all make[2]: Entering directory '/build/fastml-3.1/libs' @@ -2291,11 +2325,11 @@ cp indelCoder ../../bin/indelCoder make[3]: Entering directory '/build/fastml-3.1/programs/fastml' mkdir -p ../../bin +make[3]: Leaving directory '/build/fastml-3.1/programs/indelCoder' cp fastml ../../bin/fastml make[3]: Entering directory '/build/fastml-3.1/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss -make[3]: Leaving directory '/build/fastml-3.1/programs/indelCoder' make[3]: Leaving directory '/build/fastml-3.1/programs/fastml' make[3]: Leaving directory '/build/fastml-3.1/programs/gainLoss' make[2]: Leaving directory '/build/fastml-3.1/programs' @@ -2325,12 +2359,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/11389/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/11389/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/54242 and its subdirectories -I: Current time: Mon May 2 16:19:54 -12 2022 -I: pbuilder-time-stamp: 1651551594 +I: removing directory /srv/workspace/pbuilder/11389 and its subdirectories +I: Current time: Wed Mar 31 12:00:01 +14 2021 +I: pbuilder-time-stamp: 1617141601