Diff of the two buildlogs: -- --- b1/build.log 2024-05-12 05:27:04.749290944 +0000 +++ b2/build.log 2024-05-12 05:28:58.768434612 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jun 13 23:47:45 -12 2025 -I: pbuilder-time-stamp: 1749901665 +I: Current time: Sun May 12 19:27:08 +14 2024 +I: pbuilder-time-stamp: 1715491628 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -35,52 +35,84 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2506447/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2027052/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 12 05:27 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2027052/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2027052/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='11b0231ab8d042f7ae53c57ae105b6bf' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2506447' - PS1='# ' - PS2='> ' + INVOCATION_ID=808d019e581d4e9c94fdd7f56ddabbe0 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=2027052 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.uXH6waPj/pbuilderrc_528X --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.uXH6waPj/b1 --logfile b1/build.log fastml_3.11-4.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.uXH6waPj/pbuilderrc_CVoe --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.uXH6waPj/b2 --logfile b2/build.log fastml_3.11-4.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 12 17:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2506447/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 11 11:23 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2027052/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +178,7 @@ Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] -Fetched 18.7 MB in 0s (94.3 MB/s) +Fetched 18.7 MB in 0s (134 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19745 files and directories currently installed.) @@ -281,7 +313,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/fastml-3.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../fastml_3.11-4_source.changes +I: user script /srv/workspace/pbuilder/2027052/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2027052/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/fastml-3.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../fastml_3.11-4_source.changes dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.11-4 dpkg-buildpackage: info: source distribution unstable @@ -297,24 +333,24 @@ make[2]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make clean cd programs;make clean +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs' +cd phylogeny && make clean make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs' cd fastml && make clean cd gainLoss && make clean cd indelCoder && make clean make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o +make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' +rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs' -cd phylogeny && make clean make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' -make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' -rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o -make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' -make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' make[4]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o +make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' +make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/libs' make[2]: Leaving directory '/build/reproducible-path/fastml-3.11' @@ -353,6 +389,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp bestAlphaManyTrees.cpp: In function 'void bestAlpha::optimizeAlphaNG_EM_PROP_n_alpha(tree&, std::vector&, std::vector&, const std::vector*>*, std::vector&, double&, int, double)': bestAlphaManyTrees.cpp:184:17: warning: variable 'ax' set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha @@ -367,7 +404,6 @@ bestAlpha.cpp:371:17: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] 371 | MDOUBLE oldA=0; | ^~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp @@ -412,10 +448,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp In file included from /usr/include/c++/13/iostream:41, from readTree.h:6, from tree.h:7, @@ -448,10 +480,10 @@ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:35: note: 'pij' was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3, inlined from 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:39:108: @@ -482,9 +514,12 @@ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:35: note: 'pij' was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp In file included from fromCountTableComponentToDistancePropEB.cpp:3: fromCountTableComponentToDistancePropEB.h: In constructor 'fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB(const std::vector >&, int, multipleStochasticProcess*, const gammaDistribution*, double, double)': fromCountTableComponentToDistancePropEB.h:29:19: warning: 'fromCountTableComponentToDistancePropEB::_nodeID' will be initialized after [-Wreorder] @@ -496,12 +531,14 @@ fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] 6 | fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)': goldmanYangModel.cpp:8:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] 8 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV): @@ -510,21 +547,12 @@ goldmanYangModel.cpp:18:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] 18 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): | ^~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:269:22: required from here -likeDist.cpp:210:13: warning: variable 'oldIntervalSize' set but not used [-Wunused-but-set-variable] - 210 | MDOUBLE oldIntervalSize = currentIntervalSize; - | ^~~~~~~~~~~~~~~ In file included from generalGammaDistributionPlusInvariant.h:9, from simulateWithDependence.h:35, from simulateWithDependence.cpp:1: @@ -534,12 +562,23 @@ generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:269:22: required from here +likeDist.cpp:210:13: warning: variable 'oldIntervalSize' set but not used [-Wunused-but-set-variable] + 210 | MDOUBLE oldIntervalSize = currentIntervalSize; + | ^~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] 306 | //* for (i=1;igetNumberOfSons()+2); // both s1 and s2 should have been skiped - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp likelihoodComputation.cpp: In function 'double likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(const tree&, const sequenceContainer&, const stochasticProcess&, const Vdouble*, unObservableData*)': likelihoodComputation.cpp:43:45: warning: 'LforMissingData' may be used uninitialized [-Wmaybe-uninitialized] 43 | LofPos = LofPos / (1- LforMissingData); @@ -565,8 +596,13 @@ likelihoodComputation.cpp:27:17: note: 'LforMissingData' was declared here 27 | MDOUBLE LforMissingData; | ^~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readTree.o readTree.cpp +In file included from /usr/include/c++/13/cassert:44, + from njConstrain.cpp:4: +njConstrain.cpp: In function 'tree::TreeNode* joinNodesToSubtree(tree&, tree::TreeNode*&, tree::TreeNode*&)': +njConstrain.cpp:92:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 92 | assert (k=fatherNode->getNumberOfSons()+2); // both s1 and s2 should have been skiped + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o recognizeFormat.o recognizeFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModel.o replacementModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o searchStatus.o searchStatus.cpp @@ -616,6 +652,8 @@ tree.cpp:182:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 182 | create_names_to_internal_nodes(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp treeUtil.cpp: In function 'std::vector getNexusTreesFromFile(const std::string&)': treeUtil.cpp:371:32: warning: variable 'itStrStart' set but not used [-Wunused-but-set-variable] 371 | string::const_iterator itStrStart = it->begin(); @@ -623,8 +661,6 @@ treeUtil.cpp:372:32: warning: variable 'itStrEnd' set but not used [-Wunused-but-set-variable] 372 | string::const_iterator itStrEnd = it->end(); | ^~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp @@ -634,6 +670,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp In file included from distanceBasedSeqs2Tree.cpp:12: bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] @@ -645,7 +682,6 @@ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp @@ -657,7 +693,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:54:25: warning: 'betaDistribution::_boundary' will be initialized after [-Wreorder] @@ -669,6 +704,7 @@ betaDistribution.cpp:23:1: warning: when initialized here [-Wreorder] 23 | betaDistribution::betaDistribution(const betaDistribution& other) : | ^~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp @@ -689,17 +725,8 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeJumps.o computeJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp -In file included from computeJumps.cpp:1: -computeJumps.h: In constructor 'computeJumps::gFunc::gFunc(double, double, double)': -computeJumps.h:59:25: warning: 'computeJumps::gFunc::_Lambda2' will be initialized after [-Wreorder] - 59 | MDOUBLE _Lambda2; - | ^~~~~~~~ -computeJumps.h:57:25: warning: 'double computeJumps::gFunc::_r' [-Wreorder] - 57 | MDOUBLE _r; - | ^~ -computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] - 256 | computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) - | ^~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp In file included from generalGammaDistributionPlusInvariant.h:9, from generalGammaDistributionPlusInvariant.cpp:1: distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] @@ -708,10 +735,6 @@ generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)': -seqeuncesFilter.cpp:141:25: warning: unused variable 'pAlph' [-Wunused-variable] - 141 | const alphabet* pAlph = sc.getAlphabet(); - | ^~~~~ In file included from gammaDistributionPlusInvariant.h:9, from gammaDistributionPlusInvariant.cpp:1: distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] @@ -720,29 +743,35 @@ gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp -In file included from /usr/include/c++/13/vector:66, - from definitions.h:18, - from seqeuncesFilter.h:5, - from seqeuncesFilter.cpp:1: -In member function 'std::vector<_Tp, _Alloc>::const_reference std::vector<_Tp, _Alloc>::operator[](size_type) const [with _Tp = int; _Alloc = std::allocator]', - inlined from 'const sequence& sequenceContainer::operator[](int) const' at sequenceContainer.h:31:81, - inlined from 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)' at seqeuncesFilter.cpp:175:16: -/usr/include/c++/13/bits/stl_vector.h:1148:41: warning: 'refID' may be used uninitialized [-Wmaybe-uninitialized] - 1148 | return *(this->_M_impl._M_start + __n); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)': -seqeuncesFilter.cpp:165:13: note: 'refID' was declared here - 165 | int refID; - | ^~~~~ +In file included from computeJumps.cpp:1: +computeJumps.h: In constructor 'computeJumps::gFunc::gFunc(double, double, double)': +computeJumps.h:59:25: warning: 'computeJumps::gFunc::_Lambda2' will be initialized after [-Wreorder] + 59 | MDOUBLE _Lambda2; + | ^~~~~~~~ +computeJumps.h:57:25: warning: 'double computeJumps::gFunc::_r' [-Wreorder] + 57 | MDOUBLE _r; + | ^~ +computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] + 256 | computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) + | ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp +seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)': +seqeuncesFilter.cpp:141:25: warning: unused variable 'pAlph' [-Wunused-variable] + 141 | const alphabet* pAlph = sc.getAlphabet(); + | ^~~~~ +In file included from GamMixtureOptimizer.cpp:3: +optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': +optGammaMixtureEM.h:76:25: warning: unused variable 'res1' [-Wunused-variable] + 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); + | ^~~~ +optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const': +optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable] + 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); + | ^~~~~~~~ suffStatGammaMixture.cpp: In member function 'void suffStatGammaMixture::computeStatistics()': suffStatGammaMixture.cpp:123:33: warning: variable 'Exp_Rk' set but not used [-Wunused-but-set-variable] 123 | MDOUBLE Exp_Rk, Exp_LogRk, sum; @@ -766,15 +795,6 @@ suffStatGammaMixture.cpp:216:17: warning: variable 'res2' set but not used [-Wunused-but-set-variable] 216 | MDOUBLE res2 = 0.0; | ^~~~ -In file included from optGammaMixtureEM.cpp:1: -optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': -optGammaMixtureEM.h:76:25: warning: unused variable 'res1' [-Wunused-variable] - 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); - | ^~~~ -optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const': -optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable] - 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); - | ^~~~~~~~ In file included from /usr/include/c++/13/vector:66, from definitions.h:18, from mixtureDistribution.h:11, @@ -794,15 +814,6 @@ mixtureDistribution.cpp:210:27: note: 'categoryInComponent' was declared here 210 | 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:76:25: warning: unused variable 'res1' [-Wunused-variable] - 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); - | ^~~~ -optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const': -optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable] - 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); - | ^~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::const_reference std::vector<_Tp, _Alloc>::operator[](size_type) const [with _Tp = double; _Alloc = std::allocator]', inlined from 'const double mixtureDistribution::getComponentProb(int) const' at mixtureDistribution.h:40:95, inlined from 'virtual const double mixtureDistribution::ratesProb(int) const' at mixtureDistribution.cpp:239:26: @@ -819,7 +830,31 @@ mixtureDistribution.cpp:228:27: note: 'categoryInComponent' was declared here 228 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp +In file included from optGammaMixtureEM.cpp:1: +optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': +optGammaMixtureEM.h:76:25: warning: unused variable 'res1' [-Wunused-variable] + 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); + | ^~~~ +optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const': +optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable] + 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); + | ^~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp +In file included from /usr/include/c++/13/vector:66, + from definitions.h:18, + from seqeuncesFilter.h:5, + from seqeuncesFilter.cpp:1: +In member function 'std::vector<_Tp, _Alloc>::const_reference std::vector<_Tp, _Alloc>::operator[](size_type) const [with _Tp = int; _Alloc = std::allocator]', + inlined from 'const sequence& sequenceContainer::operator[](int) const' at sequenceContainer.h:31:81, + inlined from 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)' at seqeuncesFilter.cpp:175:16: +/usr/include/c++/13/bits/stl_vector.h:1148:41: warning: 'refID' may be used uninitialized [-Wmaybe-uninitialized] + 1148 | return *(this->_M_impl._M_start + __n); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)': +seqeuncesFilter.cpp:165:13: note: 'refID' was declared here + 165 | int refID; + | ^~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/vector:63: @@ -847,7 +882,6 @@ mixtureDistribution.cpp:72:43: note: 'pComp' declared here 72 | generalGammaDistribution* pComp; | ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp In member function 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]', inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1286:30, @@ -871,6 +905,8 @@ mixtureDistribution.cpp:40:43: note: 'pComp' declared here 40 | generalGammaDistribution* pComp; | ^~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp @@ -1125,24 +1161,18 @@ cd fastml && make all cd gainLoss && make all cd indelCoder && make all -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' -making depend +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' making depend making depend +making depend g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoder.o indelCoder.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o character.o character.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': indelCoder.cpp:422:13: warning: unused variable 'gapNum' [-Wunused-variable] 422 | int gapNum = 1; @@ -1161,6 +1191,12 @@ character.cpp:17:13: note: 'longestGapStIndex' was declared here 17 | int longestGapStIndex; | ^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp In file included from /usr/include/c++/13/vector:66, from ../../libs/phylogeny/definitions.h:18, from character.h:4, @@ -1174,19 +1210,10 @@ character.cpp:17:13: note: 'longestGapStIndex' was declared here 17 | int longestGapStIndex; | ^~~~~~~~~~~~~~~~~ -In file included from bbAlg.h:8, - from fastml.cpp:254: -bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': -bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] - 14 | const string& _reportFileName; - | ^~~~~~~~~~~~~~~ -bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] - 13 | const int _minNumOfNodesToVisit; - | ^~~~~~~~~~~~~~~~~~~~~ -bbReport.h:10:18: warning: when initialized here [-Wreorder] - 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) - | ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp In file included from bbEvaluateSpecificAV.cpp:1: bbEvaluateSpecificAV.h: In constructor 'bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&)': bbEvaluateSpecificAV.h:34:34: warning: 'bbEvaluateSpecificAV::_sc' will be initialized after [-Wreorder] @@ -1202,8 +1229,6 @@ bbEvaluateSpecificAV.cpp:65:33: warning: unused variable 'rate' [-Wunused-variable] 65 | MDOUBLE rate = _sp.rates(categor); // the r. | ^~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp In file included from bbAlg.h:8, from bbAlg.cpp:1: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': @@ -1216,7 +1241,6 @@ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp bbAlg.h: In constructor 'bbAlg::bbAlg(const tree&, std::vector&, const sequenceContainer&, boundMethod, const std::string&, double, const distribution*)': bbAlg.h:61:23: warning: 'bbAlg::_reportFileName' will be initialized after [-Wreorder] 61 | const string& _reportFileName; @@ -1236,18 +1260,28 @@ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] 7 | bbAlg::bbAlg(const tree& et, | ^~~~~ +In file included from bbAlg.h:8, + from fastml.cpp:254: +bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': +bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] + 14 | const string& _reportFileName; + | ^~~~~~~~~~~~~~~ +bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] + 13 | const int _minNumOfNodesToVisit; + | ^~~~~~~~~~~~~~~~~~~~~ +bbReport.h:10:18: warning: when initialized here [-Wreorder] + 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) + | ^~~~~~~~~~~~~~~~~ In file included from bbEvaluateSpecificAV.h:4: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ -In file included from mainbb.h:4, - from fastml.cpp:1: -bb_options.h: At global scope: +In file included from bbfindBestAVDynProg.h:5, + from bbfindBestAVDynProg.cpp:1: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp In file included from bb_options.cpp:2: bb_options.h: In constructor 'bb_options::bb_options(int&, char**)': bb_options.h:49:16: warning: 'bb_options::reportFile' will be initialized after [-Wreorder] @@ -1322,10 +1356,6 @@ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ In file included from bbNodeOrderAlg.cpp:1: bbNodeOrderAlg.h: In constructor 'bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)': bbNodeOrderAlg.h:33:34: warning: 'bbNodeOrderAlg::_sc' will be initialized after [-Wreorder] @@ -1337,13 +1367,6 @@ bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] 8 | bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, | ^~~~~~~~~~~~~~ -In file included from bbNodeOrderAlg.h:5, - from bbAlg.h:5: -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 std::string&, int)': bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] @@ -1355,19 +1378,35 @@ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ -In file included from bbfindBestAVDynProg.h:5, - from bbfindBestAVDynProg.cpp:1: +bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp +In file included from mainbb.h:4, + from fastml.cpp:1: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] + 62 | static const string usege_splash_screen() { + | ^~~~~~~~~~~~~~~~~~~ +In file included from bbNodeOrderAlg.h:5, + from bbAlg.h:5: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] + 62 | static const string usege_splash_screen() { + | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp In file included from bbNodeOrderAlg.h:5: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ +computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': +computeMarginalReconstruction.cpp:67:25: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] + 67 | MDOUBLE likelihoodOfPos = 0; + | ^~~~~~~~~~~~~~~ +computeMarginalReconstruction.cpp:45:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] + 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bbReport.h: In constructor 'BandBReport::BandBReport(const std::string&, int, int)': bbReport.h:53:23: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder] 53 | const string& _reportFileName; @@ -1378,15 +1417,13 @@ bbReport.cpp:10:1: warning: when initialized here [-Wreorder] 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp -computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': -computeMarginalReconstruction.cpp:67:25: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] - 67 | MDOUBLE likelihoodOfPos = 0; - | ^~~~~~~~~~~~~~~ -computeMarginalReconstruction.cpp:45:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] - 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': jointNoGamma.cpp:23:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] 23 | MDOUBLE totalLikelihoodOfReconstruction = 0; @@ -1395,7 +1432,6 @@ jointNoGamma.cpp:108:33: warning: unused variable 'maxL' [-Wunused-variable] 108 | MDOUBLE maxL = VERYSMALL; | ^~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp In file included from bbAlg.h:8, from mainbb.cpp:5: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': @@ -1408,6 +1444,7 @@ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp In file included from mainbb.cpp:31: ../../libs/phylogeny/bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': ../../libs/phylogeny/bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] @@ -1419,8 +1456,6 @@ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossUtils.cpp:17: @@ -1430,12 +1465,6 @@ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from mainbb.h:4, - from mainbb.cpp:1: -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ In file included from gainLossUtils.cpp:19: gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); @@ -1476,53 +1505,7 @@ gainLossUtils.cpp:788:17: warning: unused variable 'scale' [-Wunused-variable] 788 | MDOUBLE scale; | ^~~~~ -In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, - from gainLossUtils.h:27, - from gainLossModel.h:27, - from optimizeGainLossModel.h:27, - from optimizeGainLossModel.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModel.h: In constructor 'optimizeGainLossModel::optimizeGainLossModel(const tree&, stochasticProcess&, const sequenceContainer&, bool, double, int, Vdouble*, unObservableData*)': -optimizeGainLossModel.h:87:18: warning: 'optimizeGainLossModel::_weightsUniqPatterns' will be initialized after [-Wreorder] - 87 | Vdouble* _weightsUniqPatterns; - | ^~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModel.h:86:27: warning: 'unObservableData* optimizeGainLossModel::_unObservableData_p' [-Wreorder] - 86 | unObservableData* _unObservableData_p; - | ^~~~~~~~~~~~~~~~~~~ -optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] - 20 | optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, - | ^~~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModel.cpp:85:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] - 85 | MDOUBLE sumPijQij; - | ^~~~~~~~~ -gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const std::string&)': -gainLossOptions.cpp:2111:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] - 2111 | return returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp:2098:24: note: 'returnType' was declared here - 2098 | costMatrixType returnType; - | ^~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp In file included from gainLoss.h:30, from gainLoss.cpp:20: @@ -1559,7 +1542,6 @@ ../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp In file included from gainLoss.cpp:41: bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); @@ -1591,16 +1573,6 @@ gainLoss.h:266:28: warning: 'gainLoss::_unObservableData_p' will be initialized after [-Wreorder] 266 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ -In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, - from gainLossUtils.h:27, - from gainLossModel.h:27, - from gainLossModel.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.h:240:23: warning: 'distribution* gainLoss::_lossDist' [-Wreorder] 240 | distribution* _lossDist; | ^~~~~~~~~ @@ -1625,6 +1597,23 @@ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] 63 | gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) | ^~~~~~~~ +In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, + from gainLossUtils.h:27, + from gainLossModel.h:27, + from optimizeGainLossModel.h:27, + from optimizeGainLossModel.cpp:17: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from mainbb.h:4, + from mainbb.cpp:1: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] + 62 | static const string usege_splash_screen() { + | ^~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -1641,38 +1630,23 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModel::gainLossModel(double, Vdouble, bool, bool, bool, bool)': -gainLossModel.h:108:17: warning: 'gainLossModel::_gain' will be initialized after [-Wreorder] - 108 | MDOUBLE _gain; // _Q[0][1] - | ^~~~~ -gainLossModel.h:105:17: warning: 'Vdouble gainLossModel::_freq' [-Wreorder] - 105 | Vdouble _freq; - | ^~~~~ -gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] - 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): - | ^~~~~~~~~~~~~ -gainLossModel.h:112:14: warning: 'gainLossModel::_isRootFreqEQstationary' will be initialized after [-Wreorder] - 112 | bool _isRootFreqEQstationary; - | ^~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h:111:14: warning: 'bool gainLossModel::_isReversible' [-Wreorder] - 111 | bool _isReversible; - | ^~~~~~~~~~~~~ -gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] - 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): - | ^~~~~~~~~~~~~ -gainLossModel.h:114:14: warning: 'gainLossModel::_isHGT_with_Q' will be initialized after [-Wreorder] - 114 | bool _isHGT_with_Q; - | ^~~~~~~~~~~~~ -gainLossModel.h:110:15: warning: 'q2pt* gainLossModel::_q2pt' [-Wreorder] - 110 | q2pt *_q2pt; // dont use q2p - | ^~~~~ -gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] - 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): - | ^~~~~~~~~~~~~ +optimizeGainLossModel.h: In constructor 'optimizeGainLossModel::optimizeGainLossModel(const tree&, stochasticProcess&, const sequenceContainer&, bool, double, int, Vdouble*, unObservableData*)': +optimizeGainLossModel.h:87:18: warning: 'optimizeGainLossModel::_weightsUniqPatterns' will be initialized after [-Wreorder] + 87 | Vdouble* _weightsUniqPatterns; + | ^~~~~~~~~~~~~~~~~~~~ +optimizeGainLossModel.h:86:27: warning: 'unObservableData* optimizeGainLossModel::_unObservableData_p' [-Wreorder] + 86 | unObservableData* _unObservableData_p; + | ^~~~~~~~~~~~~~~~~~~ +optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] + 20 | optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, + | ^~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)': gainLoss.cpp:604:14: warning: unused variable 'missigDataChar' [-Wunused-variable] 604 | char missigDataChar = -2; | ^~~~~~~~~~~~~~ +optimizeGainLossModel.cpp:85:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] + 85 | MDOUBLE sumPijQij; + | ^~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': gainLoss.cpp:1245:64: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ @@ -1681,6 +1655,14 @@ 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ | ^~~~~~~~~~~~~~~~~~~ | ( ) +gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': +gainLoss.cpp:1868:25: warning: unused variable 'sumPijQij' [-Wunused-variable] + 1868 | MDOUBLE sumPijQij = normalizeQ(sp); + | ^~~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': +gainLoss.cpp:1990:25: warning: unused variable 'sumPijQij' [-Wunused-variable] + 1990 | MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); + | ^~~~~~~~~ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, @@ -1692,6 +1674,7 @@ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -1724,30 +1707,6 @@ optimizeGainLossModelVV.cpp:76:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] 76 | MDOUBLE sumPijQij; | ^~~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': -gainLoss.cpp:1868:25: warning: unused variable 'sumPijQij' [-Wunused-variable] - 1868 | MDOUBLE sumPijQij = normalizeQ(sp); - | ^~~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': -gainLoss.cpp:1990:25: warning: unused variable 'sumPijQij' [-Wunused-variable] - 1990 | MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); - | ^~~~~~~~~ -gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': -gainLossUtils.cpp:312:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] - 312 | return res; - | ^~~ -gainLossUtils.cpp:285:17: note: 'res' was declared here - 285 | MDOUBLE res; - | ^~~ -In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, - from gainLossUtils.h:27, - from siteSpecificGL.cpp:23: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indelCoder.cpp: In member function 'void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)': indelCoder.cpp:175:33: warning: 'condition' may be used uninitialized [-Wmaybe-uninitialized] 175 | while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ @@ -1755,28 +1714,10 @@ indelCoder.cpp:170:22: note: 'condition' was declared here 170 | bool condition; | ^~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp -In file included from siteSpecificGL.cpp:24: -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, - from computePosteriorExpectationOfChange.cpp:25: + from gainLossModel.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ @@ -1799,6 +1740,34 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModel::gainLossModel(double, Vdouble, bool, bool, bool, bool)': +gainLossModel.h:108:17: warning: 'gainLossModel::_gain' will be initialized after [-Wreorder] + 108 | MDOUBLE _gain; // _Q[0][1] + | ^~~~~ +gainLossModel.h:105:17: warning: 'Vdouble gainLossModel::_freq' [-Wreorder] + 105 | Vdouble _freq; + | ^~~~~ +gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] + 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): + | ^~~~~~~~~~~~~ +gainLossModel.h:112:14: warning: 'gainLossModel::_isRootFreqEQstationary' will be initialized after [-Wreorder] + 112 | bool _isRootFreqEQstationary; + | ^~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h:111:14: warning: 'bool gainLossModel::_isReversible' [-Wreorder] + 111 | bool _isReversible; + | ^~~~~~~~~~~~~ +gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] + 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): + | ^~~~~~~~~~~~~ +gainLossModel.h:114:14: warning: 'gainLossModel::_isHGT_with_Q' will be initialized after [-Wreorder] + 114 | bool _isHGT_with_Q; + | ^~~~~~~~~~~~~ +gainLossModel.h:110:15: warning: 'q2pt* gainLossModel::_q2pt' [-Wreorder] + 110 | q2pt *_q2pt; // dont use q2p + | ^~~~~ +gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] + 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): + | ^~~~~~~~~~~~~ gainLoss.cpp: In member function 'double gainLoss::computeDistanceFromRootForRecent(tree&)': gainLoss.cpp:4205:14: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] 4205 | bool isRecentBiggerAncient = true; @@ -1815,26 +1784,80 @@ 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ | ^~~~~~~~~~~ | ( ) +In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, + from gainLossUtils.h:27, + from siteSpecificGL.cpp:23: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::startSimultePosteriorExpectationOfChange(int, int)': gainLoss.cpp:4951:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] 4951 | MDOUBLE sumQii = 1.0; | ^~~~~~ -gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const std::string&)': -gainLossOptions.cpp:2064:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] - 2064 | return returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp:2047:27: note: 'returnType' was declared here - 2047 | optimizationLevel returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const std::string&)': -gainLossOptions.cpp:2419:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] - 2419 | return returnType; +In file included from siteSpecificGL.cpp:24: +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const std::string&)': +gainLossOptions.cpp:2111:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] + 2111 | return returnType; | ^~~~~~~~~~ -gainLossOptions.cpp:2396:24: note: 'returnType' was declared here - 2396 | simulationType returnType; +gainLossOptions.cpp:2098:24: note: 'returnType' was declared here + 2098 | costMatrixType returnType; | ^~~~~~~~~~ +gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': +gainLossUtils.cpp:312:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] + 312 | return res; + | ^~~ +gainLossUtils.cpp:285:17: note: 'res' was declared here + 285 | MDOUBLE res; + | ^~~ +In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, + from gainLossUtils.h:27, + from gainLossModel.h:27, + from computePosteriorExpectationOfChange.cpp:25: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp In file included from gainLoss.h:30, from gainLossProject.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] @@ -1896,16 +1919,20 @@ computePosteriorExpectationOfChange.cpp:216:17: note: 'pij' was declared here 216 | MDOUBLE pij; | ^~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp -mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': -mainbb.cpp:428:108: warning: 'bm' may be used uninitialized [-Wmaybe-uninitialized] - 428 | bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); - | ^ -mainbb.cpp:423:28: note: 'bm' was declared here - 423 | bbAlg::boundMethod bm; - | ^~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp +gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const std::string&)': +gainLossOptions.cpp:2064:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] + 2064 | return returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp:2047:27: note: 'returnType' was declared here + 2047 | optimizationLevel returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const std::string&)': +gainLossOptions.cpp:2419:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] + 2419 | return returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp:2396:24: note: 'returnType' was declared here + 2396 | simulationType returnType; + | ^~~~~~~~~~ ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o ar: creating libindelCoder.a a - indelCoder.o @@ -1914,6 +1941,7 @@ a - indelCoderUtils.o a - character.o a - gaps.o +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp ranlib libindelCoder.a g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder In file included from gainLoss.h:30, @@ -1944,26 +1972,7 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o -ar: creating libfastml.a -a - fastml.o -a - bbAlg.o -a - bbComputeDownAlg.o -a - bbComputeUpAlg.o -a - bbEvaluateSpecificAV.o -a - bbfindBestAVDynProg.o -a - bbNodeOrderAlg.o -a - bb_options.o -a - bbReport.o -a - computeMarginalReconstruction.o -a - jointNoGamma.o -a - mainbb.o -a - sequenceDataDiff.o -a - suffStatComponentJointNoGamma.o -ranlib libfastml.a -g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp In file included from gainLossOptimizer.cpp:20: bblLS.h: At global scope: bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] @@ -2048,23 +2057,11 @@ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, | ^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengths(int)': gainLossOptimizer.cpp:498:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] 498 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:543:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] - 543 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:487:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] - 487 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengthsvv(int)': -gainLossOptimizer.cpp:634:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] - 634 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:677:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] - 677 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:30, from rate4siteGL.h:24, from rate4siteGL.cpp:17: @@ -2077,6 +2074,9 @@ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp:543:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] + 543 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -2093,10 +2093,20 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp:487:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] + 487 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengthsvv(int)': +gainLossOptimizer.cpp:634:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] + 634 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp:677:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] + 677 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:623:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] 623 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp rate4siteGL.h: In constructor 'rate4siteGL::rate4siteGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, unObservableData*)': rate4siteGL.h:59:14: warning: 'rate4siteGL::_tr' will be initialized after [-Wreorder] 59 | tree _tr; @@ -2114,8 +2124,14 @@ rate4siteGL.cpp:152:13: warning: unused variable 'precisionLow' [-Wunused-variable] 152 | int precisionLow = 3; | ^~~~~~~~~~~~ -make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp +mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': +mainbb.cpp:428:108: warning: 'bm' may be used uninitialized [-Wmaybe-uninitialized] + 428 | bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); + | ^ +mainbb.cpp:423:28: note: 'bm' was declared here + 423 | bbAlg::boundMethod bm; + | ^~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp In file included from gainLoss.h:30, from computeCountsGL.h:24, from computeCountsGL.cpp:17: @@ -2144,34 +2160,7 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLoss.h:30, - from gainLoss4site.h:24, - from gainLoss4site.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -In file included from gainLossUtils.h:27, - from gainLossModel.h:27, - from gainLoss.h:35: -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, VVdouble&, double, bool)': computeCountsGL.h:104:14: warning: 'computeCountsGL::_tr' will be initialized after [-Wreorder] 104 | tree _tr; @@ -2210,26 +2199,6 @@ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] 33 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ -gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::string&, unObservableData*, double)': -gainLoss4site.h:68:14: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] - 68 | tree _tr; - | ^~~ -gainLoss4site.h:61:45: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] - 61 | vector > _spVVec; //save stochasticProcess for each category - | ^~~~~~~ -gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] - 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, - | ^~~~~~~~~~~~~ -gainLoss4site.h:79:27: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] - 79 | unObservableData* _unObservableData_p; // - | ^~~~~~~~~~~~~~~~~~~ -gainLoss4site.h:78:17: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] - 78 | MDOUBLE _alphaConf; - | ^~~~~~~~~~ -gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] - 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, - | ^~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp In file included from gainLoss.h:30, from computeCorrelations.h:25, from computeCorrelations.cpp:17: @@ -2258,34 +2227,25 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp -In file included from gainLoss.h:30, - from simulateChangesAlongTree.cpp:20: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -In file included from gainLossUtils.h:27, - from gainLossModel.h:27, - from gainLoss.h:35: -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp +g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml computeCorrelations.cpp: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)': computeCorrelations.cpp:130:13: warning: unused variable 'numOfbranches' [-Wunused-variable] 130 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node @@ -2331,6 +2291,34 @@ 894 | if(!numOfSites_A == numOfSites_B){ | ^~~~~~~~~~~~~ | ( ) +In file included from gainLoss.h:30, + from gainLoss4site.h:24, + from gainLoss4site.cpp:17: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +In file included from gainLossUtils.h:27, + from gainLossModel.h:27, + from gainLoss.h:35: +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::string*)': computeCorrelations.cpp:1009:14: warning: unused variable 'isPearson' [-Wunused-variable] 1009 | bool isPearson = false; @@ -2342,6 +2330,57 @@ computeCorrelations.cpp:1347:67: warning: narrowing conversion of 'gainLossOptions::_pValueCutOffForBootStrap' from 'double' to 'float' [-Wnarrowing] 1347 | float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001}; | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +computeCorrelations.cpp:1300:14: warning: variable 'it_siteB' set but not used [-Wunused-but-set-variable] + 1300 | it_B it_siteB = it_siteA->second.begin(); + | ^~~~~~~~ +gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::string&, unObservableData*, double)': +gainLoss4site.h:68:14: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] + 68 | tree _tr; + | ^~~ +gainLoss4site.h:61:45: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] + 61 | vector > _spVVec; //save stochasticProcess for each category + | ^~~~~~~ +gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] + 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, + | ^~~~~~~~~~~~~ +gainLoss4site.h:79:27: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] + 79 | unObservableData* _unObservableData_p; // + | ^~~~~~~~~~~~~~~~~~~ +gainLoss4site.h:78:17: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] + 78 | MDOUBLE _alphaConf; + | ^~~~~~~~~~ +gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] + 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, + | ^~~~~~~~~~~~~ +make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp +In file included from gainLoss.h:30, + from simulateChangesAlongTree.cpp:20: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +In file included from gainLossUtils.h:27, + from gainLossModel.h:27, + from gainLoss.h:35: +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:30, from simulateOnePos.cpp:32: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] @@ -2353,9 +2392,6 @@ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -computeCorrelations.cpp:1300:14: warning: variable 'it_siteB' set but not used [-Wunused-but-set-variable] - 1300 | it_B it_siteB = it_siteA->second.begin(); - | ^~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -2481,13 +2517,6 @@ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): | ^~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': -gainLossOptimizer.cpp:833:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] - 833 | return res; - | ^~~ -gainLossOptimizer.cpp:820:43: note: 'res' was declared here - 820 | gainLossOptions::distributionType res; - | ^~~ In member function 'void gainLossModelNonReversible::updateQ()', inlined from 'void gainLossModelNonReversible::setMu2(double)' at gainLossModel.h:156:10, inlined from 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)' at gainLoss.cpp:1857:100: @@ -2498,6 +2527,13 @@ gainLoss.cpp:1842:17: note: 'currM2' was declared here 1842 | MDOUBLE currM2; | ^~~~~~ +gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': +gainLossOptimizer.cpp:833:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] + 833 | return res; + | ^~~ +gainLossOptimizer.cpp:820:43: note: 'res' was declared here + 820 | gainLossOptions::distributionType res; + | ^~~ gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': gainLoss.cpp:1974:39: warning: 'currGainBeta' may be used uninitialized [-Wmaybe-uninitialized] 1974 | updateGainBeta(currGainBeta,spVVec,gainDist,lossDist); @@ -2583,13 +2619,6 @@ gainLoss.cpp:2466:26: note: 'countsGL' was declared here 2466 | computeCountsGL* countsGL; | ^~~~~~~~ -computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': -computeCorrelations.cpp:505:33: warning: 'expextedFreq' may be used uninitialized [-Wmaybe-uninitialized] - 505 | if(freqOfHighCorr>expextedFreq && freqOfHighCorrexpextedFreq && freqOfHighCorr split_test.out.tmp diff split_test.out.tmp split_test.out.standard +./doubleRep > doubleRep.out.tmp +diff doubleRep.out.tmp doubleRep.out.standard ./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp diff readTreeWithComments.out.tmp readTreeWithComments.out.standard -./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp -diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard -./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp -diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard -./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp -diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard ./splitMap_test > splitMap_test.out.tmp diff splitMap_test.out.tmp splitMap_test.out.standard -./doubleRep > doubleRep.out.tmp -diff doubleRep.out.tmp doubleRep.out.standard ./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard +./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp +diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard +./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp +diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard +./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp +diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny/tests' @@ -2711,17 +2747,17 @@ make[2]: Entering directory '/build/reproducible-path/fastml-3.11/programs' cd fastml && make install cd gainLoss && make install -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' -mkdir -p ../../bin cd indelCoder && make install -cp fastml ../../bin/fastml make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' mkdir -p ../../bin cp indelCoder ../../bin/indelCoder -make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' +mkdir -p ../../bin +cp fastml ../../bin/fastml make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss +make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' @@ -2753,12 +2789,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2027052/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2027052/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/2506447 and its subdirectories -I: Current time: Fri Jun 13 23:50:03 -12 2025 -I: pbuilder-time-stamp: 1749901803 +I: removing directory /srv/workspace/pbuilder/2027052 and its subdirectories +I: Current time: Sun May 12 19:28:57 +14 2024 +I: pbuilder-time-stamp: 1715491737