Diff of the two buildlogs: -- --- b1/build.log 2023-04-10 11:26:21.980893829 +0000 +++ b2/build.log 2023-04-10 11:33:54.021818899 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 9 23:18:30 -12 2023 -I: pbuilder-time-stamp: 1681125510 +I: Current time: Mon May 13 07:49:27 +14 2024 +I: pbuilder-time-stamp: 1715536167 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./fastml_3.11.orig.tar.gz] I: copying [./fastml_3.11-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Dec 17 02:38:59 2020 -12 +gpgv: Signature made Fri Dec 18 04:38:59 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -35,11 +35,20 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/18264/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/27115/tmp/hooks/D01_modify_environment starting +debug: Running on codethink9-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 +lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash +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/27115/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27115/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + 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=8' @@ -49,38 +58,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='18264' + PPID='27115' PS1='# ' PS2='> ' 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.t8voveOh/pbuilderrc_dpzN --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.t8voveOh/b1 --logfile b1/build.log fastml_3.11-3.dsc' + 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.t8voveOh/pbuilderrc_PsUI --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.t8voveOh/b2 --logfile b2/build.log --extrapackages usrmerge fastml_3.11-3.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink10-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 7 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/18264/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/27115/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +155,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] -Fetched 18.3 MB in 1s (35.3 MB/s) +Fetched 18.3 MB in 1s (34.8 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 ... 19616 files and directories currently installed.) @@ -280,8 +289,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/fastml-3.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../fastml_3.11-3_source.changes +I: user script /srv/workspace/pbuilder/27115/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/27115/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/fastml-3.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../fastml_3.11-3_source.changes dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.11-3 dpkg-buildpackage: info: source distribution unstable @@ -303,19 +321,19 @@ cd fastml && make clean cd gainLoss && make clean cd indelCoder && make clean +make[4]: Entering directory '/build/fastml-3.11/programs/fastml' +rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Entering directory '/build/fastml-3.11/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o +make[4]: Leaving directory '/build/fastml-3.11/programs/fastml' make[4]: Entering directory '/build/fastml-3.11/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o -make[4]: Leaving directory '/build/fastml-3.11/programs/indelCoder' -make[4]: Entering directory '/build/fastml-3.11/programs/fastml' -rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o -make[4]: Leaving directory '/build/fastml-3.11/libs/phylogeny' -make[3]: Leaving directory '/build/fastml-3.11/libs' -make[4]: Leaving directory '/build/fastml-3.11/programs/fastml' make[4]: Entering directory '/build/fastml-3.11/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o +make[4]: Leaving directory '/build/fastml-3.11/programs/indelCoder' +make[4]: Leaving directory '/build/fastml-3.11/libs/phylogeny' make[4]: Leaving directory '/build/fastml-3.11/programs/gainLoss' +make[3]: Leaving directory '/build/fastml-3.11/libs' make[3]: Leaving directory '/build/fastml-3.11/programs' make[2]: Leaving directory '/build/fastml-3.11' rm -f libs/phylogeny/make.dep \ @@ -349,8 +367,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlpha.o bestAlpha.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.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 @@ -365,6 +381,8 @@ bestAlpha.cpp:371:17: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] 371 | MDOUBLE oldA=0; | ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp @@ -383,8 +401,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp In file included from computeSubstitutionCounts.cpp:1: computeSubstitutionCounts.h: In constructor 'computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer&, const tree&, multipleStochasticProcess*, std::string&, VVVdouble&, int, double, bool)': computeSubstitutionCounts.h:57:19: warning: 'computeSubstitutionCounts::_LpostPerSpPerCat' will be initialized after [-Wreorder] @@ -405,9 +421,9 @@ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 15 | computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp In file included from /usr/include/c++/12/iostream:39, from readTree.h:6, from tree.h:7, @@ -440,8 +456,9 @@ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:25: note: 'Down' was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp 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: @@ -472,6 +489,7 @@ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:25: note: 'Down' was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp @@ -483,7 +501,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp 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] @@ -495,13 +512,13 @@ fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] 6 | fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.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): @@ -510,6 +527,7 @@ goldmanYangModel.cpp:18:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] 18 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): | ^~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp @@ -526,17 +544,17 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp In file included from /usr/include/c++/12/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/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] 306 | //* for (i=1;i 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(); @@ -606,7 +625,6 @@ 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/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp @@ -614,6 +632,7 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.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] @@ -625,7 +644,6 @@ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp @@ -673,10 +691,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.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(); - | ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp In file included from computeJumps.cpp:1: computeJumps.h: In constructor 'computeJumps::gFunc::gFunc(double, double, double)': @@ -689,6 +703,33 @@ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] 256 | computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) | ^~~~~~~~~~~~ +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(); + | ^~~~~ +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; + | ^~~~~~ +suffStatGammaMixture.cpp: In member function 'double suffStatGammaMixture::computeQ()': +suffStatGammaMixture.cpp:224:25: warning: unused variable 'first' [-Wunused-variable] + 224 | MDOUBLE first = _MkVec[comp] * log(P_k); + | ^~~~~ +suffStatGammaMixture.cpp:225:25: warning: unused variable 'second' [-Wunused-variable] + 225 | MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k); + | ^~~~~~ +suffStatGammaMixture.cpp:226:25: warning: unused variable 'third' [-Wunused-variable] + 226 | MDOUBLE third = -_MkVec[comp] * gammln(alpha_k); + | ^~~~~ +suffStatGammaMixture.cpp:227:25: warning: unused variable 'fourth' [-Wunused-variable] + 227 | MDOUBLE fourth = -_AkVec[comp]*beta_k; + | ^~~~~~ +suffStatGammaMixture.cpp:228:25: warning: unused variable 'fifth' [-Wunused-variable] + 228 | MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0); + | ^~~~~ +suffStatGammaMixture.cpp:216:17: warning: variable 'res2' set but not used [-Wunused-but-set-variable] + 216 | MDOUBLE res2 = 0.0; + | ^~~~ In file included from /usr/include/c++/12/vector:64, from definitions.h:18, from mixtureDistribution.h:11, @@ -733,6 +774,7 @@ 228 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp In file included from /usr/include/c++/12/vector:64, from definitions.h:18, from seqeuncesFilter.h:5, @@ -747,31 +789,7 @@ seqeuncesFilter.cpp:165:13: note: 'refID' was declared here 165 | int refID; | ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp -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; - | ^~~~~~ -suffStatGammaMixture.cpp: In member function 'double suffStatGammaMixture::computeQ()': -suffStatGammaMixture.cpp:224:25: warning: unused variable 'first' [-Wunused-variable] - 224 | MDOUBLE first = _MkVec[comp] * log(P_k); - | ^~~~~ -suffStatGammaMixture.cpp:225:25: warning: unused variable 'second' [-Wunused-variable] - 225 | MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k); - | ^~~~~~ -suffStatGammaMixture.cpp:226:25: warning: unused variable 'third' [-Wunused-variable] - 226 | MDOUBLE third = -_MkVec[comp] * gammln(alpha_k); - | ^~~~~ -suffStatGammaMixture.cpp:227:25: warning: unused variable 'fourth' [-Wunused-variable] - 227 | MDOUBLE fourth = -_AkVec[comp]*beta_k; - | ^~~~~~ -suffStatGammaMixture.cpp:228:25: warning: unused variable 'fifth' [-Wunused-variable] - 228 | MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0); - | ^~~~~ -suffStatGammaMixture.cpp:216:17: warning: variable 'res2' set but not used [-Wunused-but-set-variable] - 216 | MDOUBLE res2 = 0.0; - | ^~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp In file included from GamMixtureOptimizer.cpp:3: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': @@ -819,6 +837,17 @@ gtrModel.cpp:5:1: warning: when initialized here [-Wreorder] 5 | gtrModel::gtrModel(const Vdouble& freq, | ^~~~~~~~ +In file included from bestGtrModelParams.cpp:3: +bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': +bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] + 175 | stochasticProcess& _sp; + | ^~~ +bestGtrModelParams.h:173:34: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] + 173 | const gammaDistribution* _pProportionDist; + | ^~~~~~~~~~~~~~~~ +bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] + 162 | C_evalGTRParamProportional( const GTRParam param, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_a2c() const': gtrModel.cpp:139:16: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 139 | return result; @@ -833,17 +862,6 @@ gtrModel.cpp:144:17: note: 'result' was declared here 144 | MDOUBLE result; | ^~~~~~ -In file included from bestGtrModelParams.cpp:3: -bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': -bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] - 175 | stochasticProcess& _sp; - | ^~~ -bestGtrModelParams.h:173:34: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] - 173 | const gammaDistribution* _pProportionDist; - | ^~~~~~~~~~~~~~~~ -bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] - 162 | C_evalGTRParamProportional( const GTRParam param, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_a2t() const': gtrModel.cpp:167:16: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 167 | return result; @@ -1063,17 +1081,6 @@ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp -indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': -indelCoder.cpp:422:13: warning: unused variable 'gapNum' [-Wunused-variable] - 422 | int gapNum = 1; - | ^~~~~~ -indelCoder.cpp: In member function 'void indelCoder::printIndelSummary()': -indelCoder.cpp:587:14: warning: unused variable 'isSIC' [-Wunused-variable] - 587 | bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; - | ^~~~~ -indelCoder.cpp:597:13: warning: unused variable 'seqLeng' [-Wunused-variable] - 597 | int seqLeng = _sc.seqLen(); - | ^~~~~~~ character.cpp: In member function 'int character::getLongestGapStIndex()': character.cpp:28:16: warning: 'longestGapStIndex' may be used uninitialized [-Wmaybe-uninitialized] 28 | return longestGapStIndex; @@ -1081,20 +1088,6 @@ 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/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp In file included from /usr/include/c++/12/vector:64, from ../../libs/phylogeny/definitions.h:18, from character.h:4, @@ -1108,6 +1101,31 @@ character.cpp:17:13: note: 'longestGapStIndex' was declared here 17 | int longestGapStIndex; | ^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp +In file included from 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) + | ^~~~~~~~~~~~~~~~~ +indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': +indelCoder.cpp:422:13: warning: unused variable 'gapNum' [-Wunused-variable] + 422 | int gapNum = 1; + | ^~~~~~ +indelCoder.cpp: In member function 'void indelCoder::printIndelSummary()': +indelCoder.cpp:587:14: warning: unused variable 'isSIC' [-Wunused-variable] + 587 | bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; + | ^~~~~ +indelCoder.cpp:597:13: warning: unused variable 'seqLeng' [-Wunused-variable] + 597 | int seqLeng = _sc.seqLen(); + | ^~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp In file included from mainbb.h:4, from fastml.cpp:1: bb_options.h: At global scope: @@ -1115,9 +1133,8 @@ 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp In file included from bbAlg.h:8, from bbAlg.cpp:1: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': @@ -1130,6 +1147,7 @@ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.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; @@ -1149,6 +1167,13 @@ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] 7 | bbAlg::bbAlg(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/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp In file included from gainLossUtils.cpp:19: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] @@ -1160,6 +1185,21 @@ 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 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] + 34 | const sequenceContainer& _sc; + | ^~~ +bbEvaluateSpecificAV.h:31:30: warning: 'const computePijGam& bbEvaluateSpecificAV::_bbcpij' [-Wreorder] + 31 | const computePijGam& _bbcpij; + | ^~~~~~~ +bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] + 3 | bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, + | ^~~~~~~~~~~~~~~~~~~~ +bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': +bbEvaluateSpecificAV.cpp:65:33: warning: unused variable 'rate' [-Wunused-variable] + 65 | MDOUBLE rate = _sp.rates(categor); // the r. + | ^~~~ gainLossUtils.cpp: In function 'void printTreeWithValuesAsBP(std::ostream&, tree::TreeNode* const&, Vstring, VVVdouble*, bool)': gainLossUtils.cpp:72:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 72 | if(probs) @@ -1167,7 +1207,6 @@ gainLossUtils.cpp:88:27: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 88 | if(probs) | ^ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp gainLossUtils.cpp: In function 'void updateGainBeta(double, std::vector >&, distribution*, distribution*, bool)': gainLossUtils.cpp:481:17: warning: variable 'normFactor' set but not used [-Wunused-but-set-variable] 481 | MDOUBLE normFactor; @@ -1188,6 +1227,11 @@ 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 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 gainLoss.cpp:41: bblLS.h: At global scope: bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] @@ -1244,12 +1288,6 @@ 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 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() { - | ^~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)': gainLoss.cpp:604:14: warning: unused variable 'missigDataChar' [-Wunused-variable] 604 | char missigDataChar = -2; @@ -1266,10 +1304,28 @@ gainLoss.cpp:1868:25: warning: unused variable 'sumPijQij' [-Wunused-variable] 1868 | MDOUBLE sumPijQij = normalizeQ(sp); | ^~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp 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); | ^~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp +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; + | ^~~~~~~~~~~~~~~~~~~~~ +gainLoss.cpp: In member function 'double gainLoss::computeDistanceNearestOTUforRecent(tree&)': +gainLoss.cpp:4283:14: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] + 4283 | bool isRecentBiggerAncient = true; + | ^~~~~~~~~~~~~~~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::multipleAllBranchesByFactorAtStart(double)': +gainLoss.cpp:4382:40: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] + 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ + | ^ +gainLoss.cpp:4382:28: note: add parentheses around left hand side expression to silence this warning + 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ + | ^~~~~~~~~~~ + | ( ) In file included from optimizeGainLossModel.h:27, from optimizeGainLossModel.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': @@ -1292,54 +1348,26 @@ optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] 20 | optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, | ^~~~~~~~~~~~~~~~~~~~~ -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] - 34 | const sequenceContainer& _sc; - | ^~~ -bbEvaluateSpecificAV.h:31:30: warning: 'const computePijGam& bbEvaluateSpecificAV::_bbcpij' [-Wreorder] - 31 | const computePijGam& _bbcpij; - | ^~~~~~~ -bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] - 3 | bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, - | ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.cpp:85:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] 85 | MDOUBLE sumPijQij; | ^~~~~~~~~ -bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': -bbEvaluateSpecificAV.cpp:65:33: warning: unused variable 'rate' [-Wunused-variable] - 65 | MDOUBLE rate = _sp.rates(categor); // the r. - | ^~~~ -indelCoder.cpp: In member function 'void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)': -indelCoder.cpp:175:33: warning: 'condition' may be used uninitialized [-Wmaybe-uninitialized] - 175 | while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -indelCoder.cpp:170:22: note: 'condition' was declared here - 170 | bool condition; - | ^~~~~~~~~ -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; - | ^~~~~~~~~~~~~~~~~~~~~ -gainLoss.cpp: In member function 'double gainLoss::computeDistanceNearestOTUforRecent(tree&)': -gainLoss.cpp:4283:14: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] - 4283 | bool isRecentBiggerAncient = true; - | ^~~~~~~~~~~~~~~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::multipleAllBranchesByFactorAtStart(double)': -gainLoss.cpp:4382:40: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] - 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ - | ^ -gainLoss.cpp:4382:28: note: add parentheses around left hand side expression to silence this warning - 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ - | ^~~~~~~~~~~ - | ( ) -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp gainLoss.cpp: In member function 'void gainLoss::startSimultePosteriorExpectationOfChange(int, int)': gainLoss.cpp:4951:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] 4951 | MDOUBLE sumQii = 1.0; | ^~~~~~ -In file included from bbEvaluateSpecificAV.h:4: -bb_options.h: At global scope: +In file included from bbNodeOrderAlg.cpp:1: +bbNodeOrderAlg.h: In constructor 'bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)': +bbNodeOrderAlg.h:33:34: warning: 'bbNodeOrderAlg::_sc' will be initialized after [-Wreorder] + 33 | const sequenceContainer& _sc; + | ^~~ +bbNodeOrderAlg.h:32:30: warning: 'const computePijGam& bbNodeOrderAlg::_cpij' [-Wreorder] + 32 | const computePijGam& _cpij; + | ^~~~~ +bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] + 8 | bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, + | ^~~~~~~~~~~~~~ +In file included from 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() { | ^~~~~~~~~~~~~~~~~~~ @@ -1350,6 +1378,13 @@ gainLossUtils.cpp:285:17: note: 'res' was declared here 285 | MDOUBLE res; | ^~~ +indelCoder.cpp: In member function 'void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)': +indelCoder.cpp:175:33: warning: 'condition' may be used uninitialized [-Wmaybe-uninitialized] + 175 | while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +indelCoder.cpp:170:22: note: 'condition' was declared here + 170 | bool condition; + | ^~~~~~~~~ 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; @@ -1364,24 +1399,12 @@ gainLossOptions.cpp:2098:24: note: 'returnType' was declared here 2098 | costMatrixType returnType; | ^~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp -In file included from bbfindBestAVDynProg.h:5, - from bbfindBestAVDynProg.cpp:1: +In file included from bbNodeOrderAlg.h:5: +bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bb_options.o bb_options.cpp -In file included from bbNodeOrderAlg.cpp:1: -bbNodeOrderAlg.h: In constructor 'bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)': -bbNodeOrderAlg.h:33:34: warning: 'bbNodeOrderAlg::_sc' will be initialized after [-Wreorder] - 33 | const sequenceContainer& _sc; - | ^~~ -bbNodeOrderAlg.h:32:30: warning: 'const computePijGam& bbNodeOrderAlg::_cpij' [-Wreorder] - 32 | const computePijGam& _cpij; - | ^~~~~ -bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] - 8 | bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, - | ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp In file included from bb_options.cpp:2: bb_options.h: In constructor 'bb_options::bb_options(int&, char**)': @@ -1457,10 +1480,34 @@ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ +In file included from bbReport.cpp:1: +bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': +bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] + 14 | const string& _reportFileName; + | ^~~~~~~~~~~~~~~ +bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] + 13 | const int _minNumOfNodesToVisit; + | ^~~~~~~~~~~~~~~~~~~~~ +bbReport.h:10:18: warning: when initialized here [-Wreorder] + 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) + | ^~~~~~~~~~~~~~~~~ bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp +bbReport.h: In constructor 'BandBReport::BandBReport(const std::string&, int, int)': +bbReport.h:53:23: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder] + 53 | const string& _reportFileName; + | ^~~~~~~~~~~~~~~ +bbReport.h:51:19: warning: 'const int BandBReport::_position' [-Wreorder] + 51 | const int _position; + | ^~~~~~~~~ +bbReport.cpp:10:1: warning: when initialized here [-Wreorder] + 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : + | ^~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o ar: creating libindelCoder.a a - indelCoder.o @@ -1472,25 +1519,6 @@ ranlib libindelCoder.a g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder make[3]: Leaving directory '/build/fastml-3.11/programs/indelCoder' -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp -In file included from bbNodeOrderAlg.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/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.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] - 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/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': computeMarginalReconstruction.cpp:67:25: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] @@ -1499,16 +1527,15 @@ 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; - | ^~~~~~~~~~~~~~~ -bbReport.h:51:19: warning: 'const int BandBReport::_position' [-Wreorder] - 51 | const int _position; - | ^~~~~~~~~ -bbReport.cpp:10:1: warning: when initialized here [-Wreorder] - 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : - | ^~~~~~~~~~~ +jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': +jointNoGamma.cpp:23:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] + 23 | MDOUBLE totalLikelihoodOfReconstruction = 0; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +jointNoGamma.cpp: In member function 'std::vector jointNoGamma::computeJointAncestralFromSSC(int, const suffStatGlobalHomPos&, const suffStatGlobalHomPosJointNoGamma&, doubleRep&)': +jointNoGamma.cpp:108:33: warning: unused variable 'maxL' [-Wunused-variable] + 108 | MDOUBLE maxL = VERYSMALL; + | ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp In file included from optimizeGainLossModelVV.h:27, from optimizeGainLossModelVV.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': @@ -1534,17 +1561,9 @@ optimizeGainLossModelVV.cpp:258:41: warning: unused variable 'currentlogL' [-Wunused-variable] 258 | MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); | ^~~~~~~~~~~ -jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': -jointNoGamma.cpp:23:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] - 23 | MDOUBLE totalLikelihoodOfReconstruction = 0; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.cpp:76:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] 76 | MDOUBLE sumPijQij; | ^~~~~~~~~ -jointNoGamma.cpp: In member function 'std::vector jointNoGamma::computeJointAncestralFromSSC(int, const suffStatGlobalHomPos&, const suffStatGlobalHomPosJointNoGamma&, doubleRep&)': -jointNoGamma.cpp:108:33: warning: unused variable 'maxL' [-Wunused-variable] - 108 | MDOUBLE maxL = VERYSMALL; - | ^~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp In file included from gainLossModel.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': @@ -1585,7 +1604,17 @@ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): | ^~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp +In file included from siteSpecificGL.cpp:24: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bbAlg.h:8, from mainbb.cpp:5: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': @@ -1609,16 +1638,16 @@ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp In file included from mainbb.h:4, from mainbb.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp -In file included from siteSpecificGL.cpp:24: +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp +In file included from computePosteriorExpectationOfChange.cpp:25: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] @@ -1629,7 +1658,19 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp +In file included from gainLoss.h:35, + from gainLossProject.cpp:17: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp In file included from /usr/include/c++/12/iostream:39, from ../../libs/phylogeny/readTree.h:6, from ../../libs/phylogeny/tree.h:7, @@ -1664,18 +1705,15 @@ gainLoss.cpp:1842:17: note: 'currM2' was declared here 1842 | MDOUBLE currM2; | ^~~~~~ -In file included from computePosteriorExpectationOfChange.cpp:25: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp +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; + | ^~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp 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 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)' at gainLoss.cpp:2005:17: /usr/include/c++/12/ostream:221:25: warning: 'currTheta' may be used uninitialized [-Wmaybe-uninitialized] @@ -1739,27 +1777,8 @@ gainLoss.cpp:1929:17: note: 'bestGainBeta' was declared here 1929 | MDOUBLE bestGainBeta=1; | ^~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp -In file included from gainLoss.h:35, - from gainLossProject.cpp:17: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: 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::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; - | ^~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp In file included from gainLoss.h:35, from gainLossOptimizer.h:24, from gainLossOptimizer.cpp:17: @@ -1773,6 +1792,40 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/iostream:39, + from ../../libs/phylogeny/readTree.h:6, + from ../../libs/phylogeny/tree.h:7, + from ../../libs/phylogeny/simulateJumpsAbstract.h:5, + from ../../libs/phylogeny/simulateJumps.h:4, + from computePosteriorExpectationOfChange.h:24, + from computePosteriorExpectationOfChange.cpp:17: +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 computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:233:3: +/usr/include/c++/12/ostream:221:25: warning: 'pij' may be used uninitialized [-Wmaybe-uninitialized] + 221 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': +computePosteriorExpectationOfChange.cpp:216:17: note: 'pij' was declared here + 216 | MDOUBLE pij; + | ^~~ +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 computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:233:3: +/usr/include/c++/12/ostream:221:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] + 221 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': +computePosteriorExpectationOfChange.cpp:215:33: note: 'Up' was declared here + 215 | doubleRep resDXY, Down, Up; + | ^~ +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 computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:233:3: +/usr/include/c++/12/ostream:221:25: warning: 'Down' may be used uninitialized [-Wmaybe-uninitialized] + 221 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': +computePosteriorExpectationOfChange.cpp:215:27: note: 'Down' was declared here + 215 | doubleRep resDXY, Down, Up; + | ^~~~ 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] @@ -1857,41 +1910,6 @@ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, | ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/iostream:39, - from ../../libs/phylogeny/readTree.h:6, - from ../../libs/phylogeny/tree.h:7, - from ../../libs/phylogeny/simulateJumpsAbstract.h:5, - from ../../libs/phylogeny/simulateJumps.h:4, - from computePosteriorExpectationOfChange.h:24, - from computePosteriorExpectationOfChange.cpp:17: -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 computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:233:3: -/usr/include/c++/12/ostream:221:25: warning: 'pij' may be used uninitialized [-Wmaybe-uninitialized] - 221 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': -computePosteriorExpectationOfChange.cpp:216:17: note: 'pij' was declared here - 216 | MDOUBLE pij; - | ^~~ -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 computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:233:3: -/usr/include/c++/12/ostream:221:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] - 221 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': -computePosteriorExpectationOfChange.cpp:215:33: note: 'Up' was declared here - 215 | doubleRep resDXY, Down, Up; - | ^~ -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 computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:233:3: -/usr/include/c++/12/ostream:221:25: warning: 'Down' may be used uninitialized [-Wmaybe-uninitialized] - 221 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': -computePosteriorExpectationOfChange.cpp:215:27: note: 'Down' was declared here - 215 | doubleRep resDXY, Down, Up; - | ^~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.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); @@ -1925,6 +1943,19 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from gainLoss.h:35, + from computeCountsGL.h:24, + from computeCountsGL.cpp:17: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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; @@ -1942,46 +1973,6 @@ rate4siteGL.cpp:152:13: warning: unused variable 'precisionLow' [-Wunused-variable] 152 | int precisionLow = 3; | ^~~~~~~~~~~~ -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 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3897:53: -/usr/include/c++/12/ostream:221:25: warning: 'Theta' may be used uninitialized [-Wmaybe-uninitialized] - 221 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)': -gainLoss.cpp:3852:37: note: 'Theta' was declared here - 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; - | ^~~~~ -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 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3897:41: -/usr/include/c++/12/ostream:221:25: warning: 'Loss' may be used uninitialized [-Wmaybe-uninitialized] - 221 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)': -gainLoss.cpp:3852:32: note: 'Loss' was declared here - 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; - | ^~~~ -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 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3897:12: -/usr/include/c++/12/ostream:221:25: warning: 'AlphaRate' may be used uninitialized [-Wmaybe-uninitialized] - 221 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)': -gainLoss.cpp:3852:17: note: 'AlphaRate' was declared here - 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; - | ^~~~~~~~~ -In file included from gainLoss.h:35, - from computeCountsGL.h:24, - from computeCountsGL.cpp:17: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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; @@ -2020,20 +2011,6 @@ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] 33 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp -gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()': -gainLoss.cpp:3980:73: warning: 'AlphaLoss' may be used uninitialized [-Wmaybe-uninitialized] - 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); - | ~~~~~~~~~~^~~~~~~~~~~ -gainLoss.cpp:3947:27: note: 'AlphaLoss' was declared here - 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; - | ^~~~~~~~~ -gainLoss.cpp:3980:73: warning: 'AlphaGain' may be used uninitialized [-Wmaybe-uninitialized] - 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); - | ~~~~~~~~~~^~~~~~~~~~~ -gainLoss.cpp:3947:17: note: 'AlphaGain' was declared here - 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; - | ^~~~~~~~~ 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); @@ -2041,7 +2018,34 @@ mainbb.cpp:423:28: note: 'bm' was declared here 423 | bbAlg::boundMethod bm; | ^~ -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp +In 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 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3897:53: +/usr/include/c++/12/ostream:221:25: warning: 'Theta' may be used uninitialized [-Wmaybe-uninitialized] + 221 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)': +gainLoss.cpp:3852:37: note: 'Theta' was declared here + 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; + | ^~~~~ +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 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3897:41: +/usr/include/c++/12/ostream:221:25: warning: 'Loss' may be used uninitialized [-Wmaybe-uninitialized] + 221 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)': +gainLoss.cpp:3852:32: note: 'Loss' was declared here + 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; + | ^~~~ +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 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3897:12: +/usr/include/c++/12/ostream:221:25: warning: 'AlphaRate' may be used uninitialized [-Wmaybe-uninitialized] + 221 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)': +gainLoss.cpp:3852:17: note: 'AlphaRate' was declared here + 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; + | ^~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp 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 @@ -2060,7 +2064,23 @@ a - suffStatComponentJointNoGamma.o ranlib libfastml.a g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp +make[3]: Leaving directory '/build/fastml-3.11/programs/fastml' g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp +gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()': +gainLoss.cpp:3980:73: warning: 'AlphaLoss' may be used uninitialized [-Wmaybe-uninitialized] + 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); + | ~~~~~~~~~~^~~~~~~~~~~ +gainLoss.cpp:3947:27: note: 'AlphaLoss' was declared here + 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; + | ^~~~~~~~~ +gainLoss.cpp:3980:73: warning: 'AlphaGain' may be used uninitialized [-Wmaybe-uninitialized] + 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); + | ~~~~~~~~~~^~~~~~~~~~~ +gainLoss.cpp:3947:17: note: 'AlphaGain' was declared here + 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; + | ^~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp In file included from gainLoss.h:35, from computeCorrelations.h:25, from computeCorrelations.cpp:17: @@ -2074,8 +2094,31 @@ 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -make[3]: Leaving directory '/build/fastml-3.11/programs/fastml' -g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp +In file included from gainLoss.h:35, + from gainLoss4site.h:24, + from gainLoss4site.cpp:17: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from gainLoss.h:35, + from simulateChangesAlongTree.cpp:20: +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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 @@ -2135,19 +2178,6 @@ 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(); | ^~~~~~~~ -In file included from gainLoss.h:35, - from gainLoss4site.h:24, - from gainLoss4site.cpp:17: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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; @@ -2168,7 +2198,7 @@ 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, | ^~~~~~~~~~~~~ In file included from gainLoss.h:35, - from simulateChangesAlongTree.cpp:20: + from simulateOnePos.cpp:32: 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] @@ -2186,25 +2216,6 @@ gainLossOptimizer.cpp:820:43: note: 'res' was declared here 820 | gainLossOptions::distributionType res; | ^~~ -In file included from gainLoss.h:35, - from simulateOnePos.cpp:32: -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::startStochasticProcess()': -gainLoss.cpp:869:30: warning: 'rateDist' may be used uninitialized [-Wmaybe-uninitialized] - 869 | if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted - | ^~~~~~~~ -gainLoss.cpp:806:23: note: 'rateDist' was declared here - 806 | distribution* rateDist; - | ^~~~~~~~ In file included from simulateOnePos.cpp:18: simulateOnePos.h: In constructor 'simulateOnePos::simulateOnePos(std::string, std::ostream*, std::ostream*, int, std::string, double, double, bool, stochasticProcess*, tree*, Vdouble*, Vdouble*)': simulateOnePos.h:72:14: warning: 'simulateOnePos::_simulateNullModel' will be initialized after [-Wreorder] @@ -2242,13 +2253,6 @@ 202 | MDOUBLE sumQii = 1.0; | ^~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp -gainLoss.cpp: In member function 'void gainLoss::startStochasticProcessVec()': -gainLoss.cpp:1127:46: warning: 'rateDist' may be used uninitialized [-Wmaybe-uninitialized] - 1127 | if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted - | ^~~~~~~~ -gainLoss.cpp:1105:39: note: 'rateDist' was declared here - 1105 | distribution* rateDist; - | ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp In file included from bblLS.cpp:17: bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] @@ -2285,13 +2289,6 @@ bblLS.cpp:112:21: warning: NULL used in arithmetic [-Wpointer-arith] 112 | if (curL == NULL) | ^~~~ -gainLoss.cpp: In member function 'void gainLoss::computeCoEvolutionScoresBasedOnSimulatedData(sequenceContainer&)': -gainLoss.cpp:2511:29: warning: 'countsGL' may be used uninitialized [-Wmaybe-uninitialized] - 2511 | if(countsGL) delete countsGL; - | ^~~~~~~~ -gainLoss.cpp:2466:26: note: 'countsGL' was declared here - 2466 | computeCountsGL* countsGL; - | ^~~~~~~~ In file included from sankoffReconstructGL.cpp:17: sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)': sankoffReconstructGL.h:85:16: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] @@ -2312,6 +2309,27 @@ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): | ^~~~~~~~~~~~~~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::startStochasticProcess()': +gainLoss.cpp:869:30: warning: 'rateDist' may be used uninitialized [-Wmaybe-uninitialized] + 869 | if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted + | ^~~~~~~~ +gainLoss.cpp:806:23: note: 'rateDist' was declared here + 806 | distribution* rateDist; + | ^~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::startStochasticProcessVec()': +gainLoss.cpp:1127:46: warning: 'rateDist' may be used uninitialized [-Wmaybe-uninitialized] + 1127 | if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted + | ^~~~~~~~ +gainLoss.cpp:1105:39: note: 'rateDist' was declared here + 1105 | distribution* rateDist; + | ^~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::computeCoEvolutionScoresBasedOnSimulatedData(sequenceContainer&)': +gainLoss.cpp:2511:29: warning: 'countsGL' may be used uninitialized [-Wmaybe-uninitialized] + 2511 | if(countsGL) delete countsGL; + | ^~~~~~~~ +gainLoss.cpp:2466:26: note: 'countsGL' was declared here + 2466 | computeCountsGL* countsGL; + | ^~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': gainLoss.cpp:1195:24: warning: 'pDm' may be used uninitialized [-Wmaybe-uninitialized] 1195 | delete pDm; @@ -2364,15 +2382,15 @@ cd fastml && make test cd gainLoss && make test cd indelCoder && make test +make[3]: Entering directory '/build/fastml-3.11/programs/indelCoder' +if [ -d tests ] ; then cd tests && make -k ; fi make[3]: Entering directory '/build/fastml-3.11/programs/fastml' if [ -d tests ] ; then cd tests && make -k ; fi +make[3]: Leaving directory '/build/fastml-3.11/programs/indelCoder' make[3]: Leaving directory '/build/fastml-3.11/programs/fastml' make[3]: Entering directory '/build/fastml-3.11/programs/gainLoss' if [ -d tests ] ; then cd tests && make -k ; fi make[3]: Leaving directory '/build/fastml-3.11/programs/gainLoss' -make[3]: Entering directory '/build/fastml-3.11/programs/indelCoder' -if [ -d tests ] ; then cd tests && make -k ; fi -make[3]: Leaving directory '/build/fastml-3.11/programs/indelCoder' make[2]: Leaving directory '/build/fastml-3.11/programs' make[3]: Entering directory '/build/fastml-3.11/libs/phylogeny' cd tests; make -k test @@ -2390,20 +2408,20 @@ ./doubleRep > doubleRep.out.tmp diff split_test.out.tmp split_test.out.standard diff doubleRep.out.tmp doubleRep.out.standard +./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp +./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp +diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard +diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard ./splitMap_test > splitMap_test.out.tmp diff splitMap_test.out.tmp splitMap_test.out.standard -./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp +./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp +diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard ./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp -diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard -./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp -diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard -./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp -diff readTreeWithComments.out.tmp readTreeWithComments.out.standard ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard -./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp -diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard +./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp +diff readTreeWithComments.out.tmp readTreeWithComments.out.standard make[4]: Leaving directory '/build/fastml-3.11/libs/phylogeny/tests' make[3]: Leaving directory '/build/fastml-3.11/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.11/libs' @@ -2429,13 +2447,13 @@ cd indelCoder && make install make[3]: Entering directory '/build/fastml-3.11/programs/indelCoder' mkdir -p ../../bin +cp indelCoder ../../bin/indelCoder make[3]: Entering directory '/build/fastml-3.11/programs/fastml' mkdir -p ../../bin -cp indelCoder ../../bin/indelCoder make[3]: Entering directory '/build/fastml-3.11/programs/gainLoss' mkdir -p ../../bin -cp gainLoss ../../bin/gainLoss make[3]: Leaving directory '/build/fastml-3.11/programs/indelCoder' +cp gainLoss ../../bin/gainLoss cp fastml ../../bin/fastml make[3]: Leaving directory '/build/fastml-3.11/programs/fastml' make[3]: Leaving directory '/build/fastml-3.11/programs/gainLoss' @@ -2459,8 +2477,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'fastml' in '../fastml_3.11-3_arm64.deb'. dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.11-3_arm64.deb'. +dpkg-deb: building package 'fastml' in '../fastml_3.11-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../fastml_3.11-3_arm64.buildinfo dpkg-genchanges --build=binary -O../fastml_3.11-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2468,12 +2486,14 @@ 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/27115/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27115/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/18264 and its subdirectories -I: Current time: Sun Apr 9 23:26:20 -12 2023 -I: pbuilder-time-stamp: 1681125980 +I: removing directory /srv/workspace/pbuilder/27115 and its subdirectories +I: Current time: Mon May 13 07:56:53 +14 2024 +I: pbuilder-time-stamp: 1715536613