Diff of the two buildlogs: -- --- b1/build.log 2020-08-06 00:01:36.876705880 +0000 +++ b2/build.log 2020-08-06 00:03:15.145662714 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Aug 5 11:53:39 -12 2020 -I: pbuilder-time-stamp: 1596671619 +I: Current time: Wed Sep 8 20:24:37 +14 2021 +I: pbuilder-time-stamp: 1631082277 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ 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 @@ -37,138 +37,172 @@ dpkg-source: info: applying g++-6.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22229/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/29493/tmp/hooks/D01_modify_environment starting +debug: Running on profitbricks-build6-i386. +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/29493/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/29493/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=18' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='18642c208f0d402f82c0e16476407f8b' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='22229' - PS1='# ' - PS2='> ' + INVOCATION_ID=fa9c3c047b244181a868fd5197b1d126 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=29493 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.QWhZmCr6tP/pbuilderrc_QMJk --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.QWhZmCr6tP/b1 --logfile b1/build.log fastml_3.1-4.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.QWhZmCr6tP/pbuilderrc_NUIz --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.QWhZmCr6tP/b2 --logfile b2/build.log fastml_3.1-4.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux profitbricks-build12-i386 4.19.0-10-686-pae #1 SMP Debian 4.19.132-1 (2020-07-24) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-10-amd64 #1 SMP Debian 4.19.132-1 (2020-07-24) x86_64 GNU/Linux I: ls -l /bin - total 5492 - -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38280 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 38280 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 17768 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 38692 Feb 28 2019 cat - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown - -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp - -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash - -rwxr-xr-x 1 root root 120676 Feb 28 2019 date - -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd - -rwxr-xr-x 1 root root 100620 Feb 28 2019 df - -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir - -rwxr-xr-x 1 root root 79412 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 34532 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 34532 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 30112 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 206392 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 100952 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln - -rwxr-xr-x 1 root root 55400 Jul 26 2018 login - -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls - -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 42348 Jan 9 2019 more - -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount - -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 157832 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 38660 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm - -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 3 20:26 sh -> dash - -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty - -rwsr-xr-x 1 root root 71072 Jan 9 2019 su - -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync - -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar - -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch - -rwxr-xr-x 1 root root 34532 Feb 28 2019 true - -rwxr-xr-x 1 root root 17768 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount - -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34208 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/22229/tmp/hooks/D02_print_environment finished + total 5476 + -rwxr-xr-x 1 root root 1302248 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38280 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 38280 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 17768 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 38692 Mar 1 2019 cat + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 63268 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chown + -rwxr-xr-x 1 root root 153732 Mar 1 2019 cp + -rwxr-xr-x 1 root root 132820 Jan 18 2019 dash + -rwxr-xr-x 1 root root 120676 Mar 1 2019 date + -rwxr-xr-x 1 root root 92040 Mar 1 2019 dd + -rwxr-xr-x 1 root root 100620 Mar 1 2019 df + -rwxr-xr-x 1 root root 149736 Mar 1 2019 dir + -rwxr-xr-x 1 root root 79412 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 34532 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 34532 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 67700 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 30112 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 206392 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 100952 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 21916 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 79752 Mar 1 2019 ln + -rwxr-xr-x 1 root root 55400 Jul 27 2018 login + -rwxr-xr-x 1 root root 149736 Mar 1 2019 ls + -rwxr-xr-x 1 root root 112032 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 87972 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 79748 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 46916 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 42348 Jan 10 2019 more + -rwsr-xr-x 1 root root 50592 Jan 10 2019 mount + -rwxr-xr-x 1 root root 13724 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 157832 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 38660 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 46852 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 75588 Mar 1 2019 rm + -rwxr-xr-x 1 root root 42756 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 22276 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 8 20:24 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 8 04:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 34532 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 79652 Mar 1 2019 stty + -rwsr-xr-x 1 root root 71072 Jan 10 2019 su + -rwxr-xr-x 1 root root 34564 Mar 1 2019 sync + -rwxr-xr-x 1 root root 504024 Apr 24 2019 tar + -rwxr-xr-x 1 root root 13860 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 104292 Mar 1 2019 touch + -rwxr-xr-x 1 root root 34532 Mar 1 2019 true + -rwxr-xr-x 1 root root 17768 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 30108 Jan 10 2019 umount + -rwxr-xr-x 1 root root 34532 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 149736 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34208 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/29493/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -237,7 +271,7 @@ Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] -Fetched 19.4 MB in 3s (5563 kB/s) +Fetched 19.4 MB in 0s (84.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) @@ -392,7 +426,7 @@ 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 @@ -404,29 +438,29 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/fastml-3.1' dh_auto_clean - make -j10 clean + make -j18 clean make[2]: Entering directory '/build/fastml-3.1' cd libs;make clean cd programs;make clean -make[3]: Entering directory '/build/fastml-3.1/programs' -cd fastml && make clean make[3]: Entering directory '/build/fastml-3.1/libs' cd phylogeny && make clean +make[3]: Entering directory '/build/fastml-3.1/programs' +cd fastml && make clean cd gainLoss && make clean cd indelCoder && make clean -make[4]: Entering directory '/build/fastml-3.1/libs/phylogeny' -rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.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]: 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]: Leaving directory '/build/fastml-3.1/programs/gainLoss' +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/gainLoss' +rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.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]: Leaving directory '/build/fastml-3.1/programs/indelCoder' -make[4]: Leaving directory '/build/fastml-3.1/libs/phylogeny' +make[4]: Leaving directory '/build/fastml-3.1/programs/gainLoss' make[3]: Leaving directory '/build/fastml-3.1/programs' +make[4]: Leaving directory '/build/fastml-3.1/libs/phylogeny' make[3]: Leaving directory '/build/fastml-3.1/libs' make[2]: Leaving directory '/build/fastml-3.1' rm -f libs/phylogeny/make.dep \ @@ -441,7 +475,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j10 "INSTALL=install --strip-program=true" + make -j18 "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' @@ -460,11 +494,15 @@ 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 bestAlpha.o bestAlpha.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 bestAlphaManyTrees.o bestAlphaManyTrees.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 bestHKYparam.o bestHKYparam.cpp -bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)': -bestAlpha.cpp:371:10: 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 bootstrap.o bootstrap.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 bblEM.o bblEM.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 bblEMfixRoot.o bblEMfixRoot.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 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 +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 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 @@ -475,14 +513,10 @@ bestAlphaManyTrees.cpp:184:16: warning: variable 'cx' set but not used [-Wunused-but-set-variable] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha ^~ -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 bblEM.o bblEM.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 bblEMfixRoot.o bblEMfixRoot.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 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 -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 +bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)': +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 codon.o codon.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 codonJC.o codonJC.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 computeCounts.o computeCounts.cpp @@ -493,6 +527,8 @@ 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 computeUpAlgFactors.o computeUpAlgFactors.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 computeSubstitutionCounts.o computeSubstitutionCounts.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 computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.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 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 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] @@ -514,8 +550,6 @@ 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 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 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 @@ -534,6 +568,9 @@ 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 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 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 +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 granthamChemicalDistances.o granthamChemicalDistances.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] @@ -545,14 +582,12 @@ 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 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 -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 granthamChemicalDistances.o granthamChemicalDistances.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 hky.o hky.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 simulateWithDependence.o simulateWithDependence.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 KH_calculation.o KH_calculation.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 likeDist.o likeDist.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 likeDistfixRoot.o likeDistfixRoot.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 likeDistProp.o likeDistProp.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): @@ -561,27 +596,23 @@ 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 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 +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 +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 molphyFormat.o molphyFormat.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 likeDist.cpp:210:13: warning: variable 'oldIntervalSize' set but not used [-Wunused-but-set-variable] MDOUBLE oldIntervalSize = currentIntervalSize; ^~~~~~~~~~~~~~~ -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 -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 molphyFormat.o molphyFormat.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 nexusFormat.o nexusFormat.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 nj.o nj.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 njConstrain.o njConstrain.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 nucJC.o nucJC.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 nucleotide.o nucleotide.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 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 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); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 replacementModel.o replacementModel.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]; - ^ -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 searchStatus.o searchStatus.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 seqContainerTreeMap.o seqContainerTreeMap.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 sequence.o sequence.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 sequenceContainer.o sequenceContainer.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 simulateTree.o simulateTree.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 siteSpecificRate.o siteSpecificRate.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 someUtil.o someUtil.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 siteSpecificRate.o siteSpecificRate.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 someUtil.o someUtil.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 split.o split.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 splitMap.o splitMap.cpp 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; @@ -638,6 +656,8 @@ 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 split.o split.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 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 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 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 @@ -646,6 +666,28 @@ 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 +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 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 +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]; + ^ +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 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 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()) @@ -653,8 +695,6 @@ 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 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 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(); @@ -662,12 +702,6 @@ 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 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 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 @@ -675,6 +709,7 @@ 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 indelModel.o indelModel.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 mulAlphabet.o mulAlphabet.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 replacementModelSSRV.o replacementModelSSRV.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 stochasticProcessSSRV.o stochasticProcessSSRV.cpp In file included from distanceBasedSeqs2Tree.cpp:12: bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': bestGtrModelParams.h:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] @@ -686,7 +721,6 @@ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] C_evalGTRParamProportional( const GTRParam param, ^~~~~~~~~~~~~~~~~~~~~~~~~~ -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 stochasticProcessSSRV.o stochasticProcessSSRV.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 bestAlphaAndNu.o bestAlphaAndNu.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 C_evalParamUSSRV.o C_evalParamUSSRV.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 matrixUtils.o matrixUtils.cpp @@ -695,6 +729,9 @@ 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] @@ -706,9 +743,6 @@ 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 @@ -732,6 +766,10 @@ 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 optGammaMixtureLS.o optGammaMixtureLS.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 mixtureDistribution.o mixtureDistribution.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 suffStatGammaMixture.o suffStatGammaMixture.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 GamMixtureOptimizer.o GamMixtureOptimizer.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 optGammaMixtureEM.o optGammaMixtureEM.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 gainLossAlphabet.o gainLossAlphabet.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 wYangModel.o wYangModel.cpp In file included from computeJumps.cpp:1: computeJumps.h: In constructor 'computeJumps::gFunc::gFunc(double, double, double)': computeJumps.h:59:11: warning: 'computeJumps::gFunc::_Lambda2' will be initialized after [-Wreorder] @@ -743,11 +781,30 @@ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] 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 GamMixtureOptimizer.o GamMixtureOptimizer.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 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))); + ^~~~~~~~ +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))); + ^~~~~~~~ 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; @@ -790,17 +847,6 @@ mixtureDistribution.cpp:228:20: note: 'categoryInComponent' was declared here int componentNum, categoryInComponent, totalCat = 0; ^~~~~~~~~~~~~~~~~~~ -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))); - ^~~~~~~~ -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 optGammaMixtureEM.o optGammaMixtureEM.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 gainLossAlphabet.o gainLossAlphabet.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)': @@ -810,18 +856,6 @@ 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 wYangModel.o wYangModel.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 codonUtils.o codonUtils.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 likelihoodComputation2Codon.o likelihoodComputation2Codon.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 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 @@ -835,6 +869,8 @@ 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 fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.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 gtrModel.o gtrModel.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 bestGtrModelParams.o bestGtrModelParams.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 simulateRateShiftJumps.o simulateRateShiftJumps.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 integerAlphabet.o integerAlphabet.cpp In file included from gtrModel.cpp:1: gtrModel.h: In constructor 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)': gtrModel.h:54:10: warning: 'gtrModel::_g2t' will be initialized after [-Wreorder] @@ -846,8 +882,17 @@ gtrModel.cpp:5:1: warning: when initialized here [-Wreorder] gtrModel::gtrModel(const Vdouble& freq, ^~~~~~~~ -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 simulateRateShiftJumps.o simulateRateShiftJumps.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 integerAlphabet.o integerAlphabet.cpp +In file included from bestGtrModelParams.cpp:3: +bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': +bestGtrModelParams.h:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] + stochasticProcess& _sp; + ^~~ +bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] + const gammaDistribution* _pProportionDist; + ^~~~~~~~~~~~~~~~ +bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] + C_evalGTRParamProportional( const GTRParam param, + ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_a2c() const': gtrModel.cpp:139:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; @@ -860,17 +905,6 @@ gtrModel.cpp:167:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^~~~~~ -In file included from bestGtrModelParams.cpp:3: -bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': -bestGtrModelParams.h:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] - stochasticProcess& _sp; - ^~~ -bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] - const gammaDistribution* _pProportionDist; - ^~~~~~~~~~~~~~~~ -bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] - C_evalGTRParamProportional( const GTRParam param, - ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_c2g() const': gtrModel.cpp:181:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; @@ -1060,8 +1094,8 @@ cd fastml && make all cd gainLoss && make all cd indelCoder && make all -make[3]: Entering directory '/build/fastml-3.1/programs/indelCoder' make[3]: Entering directory '/build/fastml-3.1/programs/fastml' +make[3]: Entering directory '/build/fastml-3.1/programs/indelCoder' make[3]: Entering directory '/build/fastml-3.1/programs/gainLoss' making depend making depend @@ -1076,6 +1110,14 @@ 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 +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 indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': indelCoder.cpp:422:6: warning: unused variable 'gapNum' [-Wunused-variable] int gapNum = 1; @@ -1095,185 +1137,6 @@ 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]){ ^ -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 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 -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 bbAlg.h:8, - from fastml.cpp:254: -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 bbNodeOrderAlg.o bbNodeOrderAlg.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.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() { - ^~~~~~~~~~~~~~~~~~~ -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 -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] - const sequenceContainer& _sc; - ^~~ -bbEvaluateSpecificAV.h:31:23: warning: 'const computePijGam& bbEvaluateSpecificAV::_bbcpij' [-Wreorder] - const computePijGam& _bbcpij; - ^~~~~~~ -bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] - bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, - ^~~~~~~~~~~~~~~~~~~~ -bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': -bbEvaluateSpecificAV.cpp:65:12: warning: unused variable 'rate' [-Wunused-variable] - MDOUBLE rate = _sp.rates(categor); // the r. - ^~~~ -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() { - ^~~~~~~~~~~~~~~~~~~ -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] - const sequenceContainer& _sc; - ^~~ -bbNodeOrderAlg.h:32:23: warning: 'const computePijGam& bbNodeOrderAlg::_cpij' [-Wreorder] - const computePijGam& _cpij; - ^~~~~ -bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] - bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, - ^~~~~~~~~~~~~~ -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 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 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 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 -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) - ^~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - MDOUBLE curL =NULL); - ^~~~ -bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] - MDOUBLE curL =NULL); - ^~~~ -bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': -bblLS.h:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] - unObservableData* _unObservableData_p; - ^~~~~~~~~~~~~~~~~~~ -bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] - Vdouble* _weights; - ^~~~~~~~ -bblLS.h:96:11: warning: when initialized here [-Wreorder] - explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, - ^~~~~~~~~~~~~~ -bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': -bblLS.h:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] - unObservableData* _unObservableData_p; - ^~~~~~~~~~~~~~~~~~~ -bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] - Vdouble* _weights; - ^~~~~~~~ -bblLS.h:152:11: warning: when initialized here [-Wreorder] - explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLoss.cpp:20: -gainLoss.h: In constructor 'gainLoss::gainLoss()': -gainLoss.h:266:21: warning: 'gainLoss::_unObservableData_p' will be initialized after [-Wreorder] - unObservableData* _unObservableData_p; - ^~~~~~~~~~~~~~~~~~~ -gainLoss.h:240:16: warning: 'distribution* gainLoss::_lossDist' [-Wreorder] - distribution* _lossDist; - ^~~~~~~~~ -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 gainLoss.cpp:20: -gainLoss.h:240:16: warning: 'gainLoss::_lossDist' will be initialized after [-Wreorder] - distribution* _lossDist; - ^~~~~~~~~ -gainLoss.h:239:16: warning: 'distribution* gainLoss::_gainDist' [-Wreorder] - distribution* _gainDist; - ^~~~~~~~~ -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 gainLoss.cpp:20: -gainLoss.h:273:12: warning: 'gainLoss::_refSeq' will be initialized after [-Wreorder] - sequence* _refSeq; // the reference sequence - ^~~~~~~ -gainLoss.h:267:11: warning: 'Vdouble* gainLoss::_weightsUniqPatterns' [-Wreorder] - Vdouble* _weightsUniqPatterns; - ^~~~~~~~~~~~~~~~~~~~ -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 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] @@ -1355,35 +1218,50 @@ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^~~~~~~~~~ -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 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 +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] + 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 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() { ^~~~~~~~~~~~~~~~~~~ -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 mainbb.o mainbb.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 bbReport.cpp:1: +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] + const sequenceContainer& _sc; + ^~~ +bbEvaluateSpecificAV.h:31:23: warning: 'const computePijGam& bbEvaluateSpecificAV::_bbcpij' [-Wreorder] + const computePijGam& _bbcpij; + ^~~~~~~ +bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] + bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, + ^~~~~~~~~~~~~~~~~~~~ +bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': +bbEvaluateSpecificAV.cpp:65:12: warning: unused variable 'rate' [-Wunused-variable] + MDOUBLE rate = _sp.rates(categor); // the r. + ^~~~ +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] + const sequenceContainer& _sc; + ^~~ +bbNodeOrderAlg.h:32:23: warning: 'const computePijGam& bbNodeOrderAlg::_cpij' [-Wreorder] + const computePijGam& _cpij; + ^~~~~ +bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] + bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, + ^~~~~~~~~~~~~~ +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; @@ -1394,40 +1272,35 @@ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ -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 ) : - ^~~~~~~~~~~ -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){ - ^~~~~~~~~~~ - ( ) -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; - ^~~~~~ jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': jointNoGamma.cpp:23:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] MDOUBLE totalLikelihoodOfReconstruction = 0; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +jointNoGamma.cpp: In member function 'std::vector jointNoGamma::computeJointAncestralFromSSC(int, const suffStatGlobalHomPos&, const suffStatGlobalHomPosJointNoGamma&, doubleRep&)': +jointNoGamma.cpp:108:12: warning: unused variable 'maxL' [-Wunused-variable] + MDOUBLE maxL = VERYSMALL; + ^~~~ +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; @@ -1435,13 +1308,9 @@ computeMarginalReconstruction.cpp:45:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] MDOUBLE totalLikelihoodOfReconstruction = 0; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -jointNoGamma.cpp: In member function 'std::vector jointNoGamma::computeJointAncestralFromSSC(int, const suffStatGlobalHomPos&, const suffStatGlobalHomPosJointNoGamma&, doubleRep&)': -jointNoGamma.cpp:108:12: warning: unused variable 'maxL' [-Wunused-variable] - 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 sequenceDataDiff.o sequenceDataDiff.cpp In file included from bbAlg.h:8, - from mainbb.cpp:5: + from fastml.cpp:254: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; @@ -1453,10 +1322,39 @@ 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 -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; - ^~~~~~~~~~ +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 bbAlg.h:8, + from mainbb.cpp:5: +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 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() { + ^~~~~~~~~~~~~~~~~~~ +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.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] @@ -1468,23 +1366,38 @@ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] C_evalGTRParamProportional( const GTRParam param, ^~~~~~~~~~~~~~~~~~~~~~~~~~ -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; - ^~~~~~~~~~ +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 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 gainLossUtils.o gainLossUtils.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.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() { + ^~~~~~~~~~~~~~~~~~~ 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 -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 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 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() { ^~~~~~~~~~~~~~~~~~~ -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 siteSpecificGL.o siteSpecificGL.cpp In file included from gainLossUtils.cpp:19: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] @@ -1500,9 +1413,11 @@ gainLossUtils.cpp:72:5: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if(probs) ^ +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 gainLossUtils.cpp:88:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if(probs) ^ +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 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; @@ -1511,6 +1426,18 @@ gainLossUtils.cpp:788:10: warning: unused variable 'scale' [-Wunused-variable] MDOUBLE scale; ^~~~~ +In file included from gainLoss.h:35, + from gainLoss.cpp:20: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:10: 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 optimizeGainLossModel.h:27, from optimizeGainLossModel.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': @@ -1537,6 +1464,7 @@ optimizeGainLossModel.cpp:85:10: 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 In file included from optimizeGainLossModelVV.h:27, from optimizeGainLossModelVV.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': @@ -1560,13 +1488,76 @@ optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, ^~~~~~~~~~~~~~~~~~~~~~~ -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 optimizeGainLossModelVV.cpp:258:13: warning: unused variable 'currentlogL' [-Wunused-variable] MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); ^~~~~~~~~~~ +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] + MDOUBLE curL =NULL); + ^~~~ +bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] + MDOUBLE curL =NULL); + ^~~~ +bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': +bblLS.h:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] + unObservableData* _unObservableData_p; + ^~~~~~~~~~~~~~~~~~~ +bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] + Vdouble* _weights; + ^~~~~~~~ +bblLS.h:96:11: warning: when initialized here [-Wreorder] + explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, + ^~~~~~~~~~~~~~ +bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': +bblLS.h:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] + unObservableData* _unObservableData_p; + ^~~~~~~~~~~~~~~~~~~ +bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] + Vdouble* _weights; + ^~~~~~~~ +bblLS.h:152:11: warning: when initialized here [-Wreorder] + explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from gainLoss.cpp:20: +gainLoss.h: In constructor 'gainLoss::gainLoss()': +gainLoss.h:266:21: warning: 'gainLoss::_unObservableData_p' will be initialized after [-Wreorder] + unObservableData* _unObservableData_p; + ^~~~~~~~~~~~~~~~~~~ +gainLoss.h:240:16: warning: 'distribution* gainLoss::_lossDist' [-Wreorder] + distribution* _lossDist; + ^~~~~~~~~ +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 gainLoss.cpp:20: +gainLoss.h:240:16: warning: 'gainLoss::_lossDist' will be initialized after [-Wreorder] + distribution* _lossDist; + ^~~~~~~~~ +gainLoss.h:239:16: warning: 'distribution* gainLoss::_gainDist' [-Wreorder] + distribution* _gainDist; + ^~~~~~~~~ +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 gainLoss.cpp:20: +gainLoss.h:273:12: warning: 'gainLoss::_refSeq' will be initialized after [-Wreorder] + sequence* _refSeq; // the reference sequence + ^~~~~~~ +gainLoss.h:267:11: warning: 'Vdouble* gainLoss::_weightsUniqPatterns' [-Wreorder] + Vdouble* _weightsUniqPatterns; + ^~~~~~~~~~~~~~~~~~~~ +gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] + gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) + ^~~~~~~~ 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 ancestralReconstructStates.o ancestralReconstructStates.cpp +gainLoss.cpp: In member function 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)': +gainLoss.cpp:604:7: warning: unused variable 'missigDataChar' [-Wunused-variable] + char missigDataChar = -2; + ^~~~~~~~~~~~~~ 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] @@ -1608,29 +1599,14 @@ 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): ^~~~~~~~~~~~~ -gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': -gainLossUtils.cpp:312:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] - return res; - ^~~ -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 siteSpecificGL.o siteSpecificGL.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 computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp -ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o -ar: creating libindelCoder.a -a - indelCoder.o -a - indelCoderOptions.o -a - indelCoderProject.o -a - indelCoderUtils.o -a - character.o -a - gaps.o -ranlib libindelCoder.a +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 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] @@ -1642,6 +1618,14 @@ 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::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 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] @@ -1653,19 +1637,6 @@ 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny indelCoder.o libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder -gainLoss.cpp: In member 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/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 gainLossProject.o gainLossProject.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 gainLossOptimizer.o gainLossOptimizer.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 ancestralReconstructStates.o ancestralReconstructStates.cpp -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 gainLossProject.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': @@ -1678,6 +1649,23 @@ 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~ +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 +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 gainLoss.h:35, from gainLossOptimizer.h:24, from gainLossOptimizer.cpp:17: @@ -1691,6 +1679,10 @@ 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~ +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; + ^~~~~~ 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] @@ -1781,6 +1773,7 @@ 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 computeCountsGL.o computeCountsGL.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); @@ -1801,28 +1794,44 @@ gainLossOptimizer.cpp:623:10: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] MDOUBLE newLnoUnObservableDataCorrection = 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 rate4siteGL.o rate4siteGL.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 computeCountsGL.o computeCountsGL.cpp +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 +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): + ^~~~~~~~~~~ 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 -ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o -ar: creating libfastml.a -a - fastml.o -a - bbAlg.o -a - bbComputeDownAlg.o -a - bbComputeUpAlg.o -a - bbEvaluateSpecificAV.o -a - bbfindBestAVDynProg.o -a - bbNodeOrderAlg.o -a - bb_options.o -a - bbReport.o -a - computeMarginalReconstruction.o -a - jointNoGamma.o -a - mainbb.o -a - sequenceDataDiff.o -a - suffStatComponentJointNoGamma.o -ranlib libfastml.a -g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny fastml.o libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml +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; + ^~~~~~~~~~~~ +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 gainLoss.h:35, from computeCountsGL.h:24, from computeCountsGL.cpp:17: @@ -1836,6 +1845,11 @@ 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~ +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 simulateOnePos.o simulateOnePos.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] @@ -1879,19 +1893,6 @@ computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): ^~~~~~~~~~~~~~~ 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 gainLoss.h:35, from computeCorrelations.h:25, from computeCorrelations.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': @@ -1904,28 +1905,14 @@ 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; - ^~~~~~~~~~~~ -computeCorrelations.cpp: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)': -computeCorrelations.cpp:130:6: warning: unused variable 'numOfbranches' [-Wunused-variable] - int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node - ^~~~~~~~~~~~~ +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; + ^~~~~~~~~~ In file included from gainLoss.h:35, from gainLoss4site.h:24, from gainLoss4site.cpp:17: @@ -1939,6 +1926,10 @@ 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~ +computeCorrelations.cpp: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)': +computeCorrelations.cpp:130:6: warning: unused variable 'numOfbranches' [-Wunused-variable] + int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node + ^~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': computeCorrelations.cpp:408:8: warning: unused variable 'isHigherNminReducedFreqOfHighCorr' [-Wunused-variable] int isHigherNminReducedFreqOfHighCorr = false; @@ -1959,6 +1950,18 @@ computeCorrelations.cpp:584:23: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^~~~ +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) + ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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; @@ -1972,14 +1975,6 @@ computeCorrelations.cpp:680:10: warning: unused variable 'isNextLowerBinAllowed' [-Wunused-variable] bool isNextLowerBinAllowed = true; ^~~~~~~~~~~~~~~~~~~~~ -computeCorrelations.cpp: In member function 'void computeCorrelations::produceSymeticMatrix(VVVdouble&, bool)': -computeCorrelations.cpp:894:19: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] - if(!numOfSites_A == numOfSites_B){ - ^~ -computeCorrelations.cpp:894:5: note: add parentheses around left hand side expression to silence this warning - if(!numOfSites_A == numOfSites_B){ - ^~~~~~~~~~~~~ - ( ) In file included from gainLoss4site.cpp:17: gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::__cxx11::string&, unObservableData*, double)': gainLoss4site.h:68:7: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] @@ -2001,6 +1996,14 @@ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, ^~~~~~~~~~~~~ +computeCorrelations.cpp: In member function 'void computeCorrelations::produceSymeticMatrix(VVVdouble&, bool)': +computeCorrelations.cpp:894:19: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] + if(!numOfSites_A == numOfSites_B){ + ^~ +computeCorrelations.cpp:894:5: note: add parentheses around left hand side expression to silence this warning + if(!numOfSites_A == numOfSites_B){ + ^~~~~~~~~~~~~ + ( ) 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; @@ -2015,58 +2018,6 @@ computeCorrelations.cpp:1300:7: warning: variable 'it_siteB' set but not used [-Wunused-but-set-variable] it_B it_siteB = it_siteA->second.begin(); ^~~~~~~~ -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 -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 simulateOnePos.o simulateOnePos.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 bblLS.o bblLS.cpp -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) - ^~~~~~~~~~~~~~~~~~~~~~~~~~ -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] -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); - ^~~~ -bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] - MDOUBLE curL =NULL); - ^~~~ -bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': -bblLS.h:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] - unObservableData* _unObservableData_p; - ^~~~~~~~~~~~~~~~~~~ -bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] - Vdouble* _weights; - ^~~~~~~~ -bblLS.h:96:11: warning: when initialized here [-Wreorder] - explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, - ^~~~~~~~~~~~~~ -bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': -bblLS.h:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] - unObservableData* _unObservableData_p; - ^~~~~~~~~~~~~~~~~~~ -bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] - Vdouble* _weights; - ^~~~~~~~ -bblLS.h:152:11: warning: when initialized here [-Wreorder] - explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:35, from simulateOnePos.cpp:32: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': @@ -2079,14 +2030,6 @@ 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~ -bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, stochasticProcess*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': -bblLS.cpp:36:14: warning: NULL used in arithmetic [-Wpointer-arith] - if (curL == NULL) - ^~~~ -bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, std::vector >&, const distribution*, const distribution*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': -bblLS.cpp:112:14: warning: NULL used in arithmetic [-Wpointer-arith] - if (curL == NULL) - ^~~~ 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] @@ -2125,6 +2068,61 @@ simulateOnePos.cpp:202:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] MDOUBLE sumQii = 1.0; ^~~~~~ +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 +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); + ^~~~ +bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] + MDOUBLE curL =NULL); + ^~~~ +bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': +bblLS.h:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] + unObservableData* _unObservableData_p; + ^~~~~~~~~~~~~~~~~~~ +bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] + Vdouble* _weights; + ^~~~~~~~ +bblLS.h:96:11: warning: when initialized here [-Wreorder] + explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, + ^~~~~~~~~~~~~~ +bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': +bblLS.h:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] + unObservableData* _unObservableData_p; + ^~~~~~~~~~~~~~~~~~~ +bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] + Vdouble* _weights; + ^~~~~~~~ +bblLS.h:152:11: warning: when initialized here [-Wreorder] + explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, stochasticProcess*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': +bblLS.cpp:36:14: warning: NULL used in arithmetic [-Wpointer-arith] + if (curL == NULL) + ^~~~ +bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, std::vector >&, const distribution*, const distribution*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': +bblLS.cpp:112:14: warning: NULL used in arithmetic [-Wpointer-arith] + if (curL == NULL) + ^~~~ +ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o +ar: creating libindelCoder.a +a - indelCoder.o +a - indelCoderOptions.o +a - indelCoderProject.o +a - indelCoderUtils.o +a - character.o +a - gaps.o +ranlib libindelCoder.a +g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny indelCoder.o libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder 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] @@ -2146,11 +2144,51 @@ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): ^~~~~~~~~~~~~~~~~~~~ +make[3]: Leaving directory '/build/fastml-3.1/programs/indelCoder' +ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o +ar: creating libfastml.a +a - fastml.o +a - bbAlg.o +a - bbComputeDownAlg.o +a - bbComputeUpAlg.o +a - bbEvaluateSpecificAV.o +a - bbfindBestAVDynProg.o +a - bbNodeOrderAlg.o +a - bb_options.o +a - bbReport.o +a - computeMarginalReconstruction.o +a - jointNoGamma.o +a - mainbb.o +a - sequenceDataDiff.o +a - suffStatComponentJointNoGamma.o +ranlib libfastml.a +g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny 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' +gainLoss.cpp: In member 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); + ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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; + ^~~~~~~~~~ +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 && freqOfHighCorr doubleRep.out.tmp diff doubleRep.out.tmp doubleRep.out.standard -./split_test > split_test.out.tmp -diff split_test.out.tmp split_test.out.standard -./splitMap_test > splitMap_test.out.tmp -diff splitMap_test.out.tmp splitMap_test.out.standard -./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp -diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard ./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp diff readTreeWithComments.out.tmp readTreeWithComments.out.standard +./splitMap_test > splitMap_test.out.tmp +diff splitMap_test.out.tmp splitMap_test.out.standard +./split_test > split_test.out.tmp +diff split_test.out.tmp split_test.out.standard ./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp -diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard ./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp +diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard ./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard +./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp +diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard make[4]: Leaving directory '/build/fastml-3.1/libs/phylogeny/tests' make[3]: Leaving directory '/build/fastml-3.1/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.1/libs' @@ -2257,7 +2291,7 @@ dh_testroot dh_prep dh_auto_install - make -j10 install DESTDIR=/build/fastml-3.1/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j18 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' @@ -2310,12 +2344,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/29493/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/29493/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/22229 and its subdirectories -I: Current time: Wed Aug 5 12:01:36 -12 2020 -I: pbuilder-time-stamp: 1596672096 +I: removing directory /srv/workspace/pbuilder/29493 and its subdirectories +I: Current time: Wed Sep 8 20:26:14 +14 2021 +I: pbuilder-time-stamp: 1631082374