Diff of the two buildlogs: -- --- b1/build.log 2025-03-02 17:58:52.819421244 +0000 +++ b2/build.log 2025-03-02 18:03:10.783712112 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Apr 4 12:20:11 -12 2026 -I: pbuilder-time-stamp: 1775348411 +I: Current time: Mon Mar 3 07:58:55 +14 2025 +I: pbuilder-time-stamp: 1740938335 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2206049/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3842789/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 2 17:59 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3842789/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3842789/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='9d315ce04dab42a9843258b42501999d' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2206049' - PS1='# ' - PS2='> ' + INVOCATION_ID=717547bec1774e4e8e2dca08731752a3 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3842789 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.ZqiolBWK/pbuilderrc_omd5 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZqiolBWK/b1 --logfile b1/build.log fastml_3.11-4.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ZqiolBWK/pbuilderrc_oFBi --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZqiolBWK/b2 --logfile b2/build.log fastml_3.11-4.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2206049/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3842789/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -142,7 +174,7 @@ Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] -Fetched 20.6 MB in 0s (140 MB/s) +Fetched 20.6 MB in 2s (8731 kB/s) Preconfiguring packages ... 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 ... 19802 files and directories currently installed.) @@ -277,7 +309,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/fastml-3.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../fastml_3.11-4_source.changes +I: user script /srv/workspace/pbuilder/3842789/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3842789/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/fastml-3.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../fastml_3.11-4_source.changes dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.11-4 dpkg-buildpackage: info: source distribution unstable @@ -289,7 +325,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/fastml-3.11' dh_auto_clean - make -j42 clean + make -j20 clean make[2]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make clean cd programs;make clean @@ -299,20 +335,20 @@ cd fastml && make clean cd gainLoss && make clean cd indelCoder && make clean -make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' -rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o +make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' +rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o -make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' -make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' +make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/libs' +make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' make[2]: Leaving directory '/build/reproducible-path/fastml-3.11' rm -f libs/phylogeny/make.dep \ programs/fastml/make.dep \ @@ -328,7 +364,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j42 "INSTALL=install --strip-program=true" + make -j20 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make all make[2]: Entering directory '/build/reproducible-path/fastml-3.11/libs' @@ -357,8 +393,22 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o clustalFormat.o clustalFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp +bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)': +bestAlpha.cpp:371:17: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] + 371 | MDOUBLE oldA=0; + | ^~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeCounts.o computeCounts.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 + | ^~ +bestAlphaManyTrees.cpp:184:20: warning: variable 'bx' set but not used [-Wunused-but-set-variable] + 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha + | ^~ +bestAlphaManyTrees.cpp:184:23: warning: variable 'cx' set but not used [-Wunused-but-set-variable] + 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha + | ^~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeDownAlg.o computeDownAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeMarginalAlg.o computeMarginalAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp @@ -370,20 +420,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.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] @@ -404,23 +440,12 @@ 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): | ^~~~~~~~~~~~~~~~~~~~~~~~~ -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 - | ^~ -bestAlphaManyTrees.cpp:184:20: warning: variable 'bx' set but not used [-Wunused-but-set-variable] - 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha - | ^~ -bestAlphaManyTrees.cpp:184:23: warning: variable 'cx' set but not used [-Wunused-but-set-variable] - 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha - | ^~ -bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)': -bestAlpha.cpp:371:17: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] - 371 | MDOUBLE oldA=0; - | ^~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp In file included from /usr/include/c++/14/iostream:41, from readTree.h:6, from tree.h:7, @@ -453,30 +478,11 @@ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:35: note: 'pij' was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.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] - 29 | const int _nodeID; - | ^~~~~~~ -fromCountTableComponentToDistancePropEB.h:28:34: warning: 'const gammaDistribution* fromCountTableComponentToDistancePropEB::_pProportionDist' [-Wreorder] - 28 | const gammaDistribution* _pProportionDist; - | ^~~~~~~~~~~~~~~~ -fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] - 6 | fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.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: @@ -507,16 +513,40 @@ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:35: note: 'pij' was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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] + 29 | const int _nodeID; + | ^~~~~~~ +fromCountTableComponentToDistancePropEB.h:28:34: warning: 'const gammaDistribution* fromCountTableComponentToDistancePropEB::_pProportionDist' [-Wreorder] + 28 | const gammaDistribution* _pProportionDist; + | ^~~~~~~~~~~~~~~~ +fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] + 6 | fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o molphyFormat.o molphyFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp In file included from generalGammaDistributionPlusInvariant.h:9, from simulateWithDependence.h:35, from simulateWithDependence.cpp:1: @@ -534,17 +564,6 @@ goldmanYangModel.cpp:18:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] 18 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): | ^~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp -numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] - 306 | //* for (i=1;igetNumberOfSons()+2); // both s1 and s2 should have been skiped + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp In member function 'virtual void generalGammaDistribution::setGammaParameters(int, double, double)', inlined from 'generalGammaDistribution::generalGammaDistribution(double, double, int)' at generalGammaDistribution.cpp:34:20: generalGammaDistribution.cpp:56:26: warning: '*this.generalGammaDistribution::_alpha' is used uninitialized [-Wuninitialized] @@ -571,30 +599,38 @@ generalGammaDistribution.cpp:56:49: warning: '*this.generalGammaDistribution::_beta' may be used uninitialized [-Wmaybe-uninitialized] 56 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories())) | ^~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp +numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] + 306 | //* for (i=1;igetNumberOfSons()+2); // both s1 and s2 should have been skiped - | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcess.o stochasticProcess.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp sequenceContainer.cpp: In member function 'void sequenceContainer::removeGapPositions()': sequenceContainer.cpp:187:14: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] 187 | bool gapCol; @@ -611,13 +647,34 @@ sequenceContainer.cpp:467:19: warning: unused variable 'len' [-Wunused-variable] 467 | const int len = _seqDataVec[0].seqLen(); | ^~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp sequence.cpp: In constructor 'sequence::sequence(const sequence&, const alphabet*)': sequence.cpp:76:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 76 | || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp +treeUtil.cpp: In function 'std::vector getNexusTreesFromFile(const std::string&)': +treeUtil.cpp:371:32: warning: variable 'itStrStart' set but not used [-Wunused-but-set-variable] + 371 | string::const_iterator itStrStart = it->begin(); + | ^~~~~~~~~~ +treeUtil.cpp:372:32: warning: variable 'itStrEnd' set but not used [-Wunused-but-set-variable] + 372 | string::const_iterator itStrEnd = it->end(); + | ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp +tree.cpp: In constructor 'tree::tree(const std::string&)': +tree.cpp:180:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 180 | if (in.is_open()) + | ^~ +tree.cpp:182:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 182 | create_names_to_internal_nodes(); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp @@ -626,42 +683,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp -tree.cpp: In constructor 'tree::tree(const std::string&)': -tree.cpp:180:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 180 | if (in.is_open()) - | ^~ -tree.cpp:182:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 182 | create_names_to_internal_nodes(); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp -likelihoodComputation.cpp: In function 'double likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(const tree&, const sequenceContainer&, const stochasticProcess&, const Vdouble*, unObservableData*)': -likelihoodComputation.cpp:43:45: warning: 'LforMissingData' may be used uninitialized [-Wmaybe-uninitialized] - 43 | LofPos = LofPos / (1- LforMissingData); - | ~~^~~~~~~~~~~~~~~~~~ -likelihoodComputation.cpp:27:17: note: 'LforMissingData' was declared here - 27 | MDOUBLE LforMissingData; - | ^~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp -treeUtil.cpp: In function 'std::vector getNexusTreesFromFile(const std::string&)': -treeUtil.cpp:371:32: warning: variable 'itStrStart' set but not used [-Wunused-but-set-variable] - 371 | string::const_iterator itStrStart = it->begin(); - | ^~~~~~~~~~ -treeUtil.cpp:372:32: warning: variable 'itStrEnd' set but not used [-Wunused-but-set-variable] - 372 | string::const_iterator itStrEnd = it->end(); - | ^~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistribution.o betaDistribution.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.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] @@ -673,6 +695,11 @@ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp In file included from pairwiseGammaDistance.h:6, from pairwiseGammaDistance.cpp:3: likeDist.h:51:19: warning: 'virtual const double likeDist::giveDistance(const sequence&, const sequence&, const std::vector*, double*) const' was hidden [-Woverloaded-virtual=] @@ -681,13 +708,17 @@ pairwiseGammaDistance.h:32:19: note: by 'const double pairwiseGammaDistance::giveDistance(const sequence&, const sequence&, const std::vector*, double*, double*) const' 32 | const MDOUBLE giveDistance(const sequence& s1, | ^~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistribution.o betaDistribution.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp In file included from betaDistribution.cpp:3: betaDistribution.h: In copy constructor 'betaDistribution::betaDistribution(const betaDistribution&)': betaDistribution.h:54:25: warning: 'betaDistribution::_boundary' will be initialized after [-Wreorder] @@ -699,6 +730,19 @@ betaDistribution.cpp:23:1: warning: when initialized here [-Wreorder] 23 | betaDistribution::betaDistribution(const betaDistribution& other) : | ^~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp +In member function 'virtual void betaDistribution::setBetaParameters(int, double, double)', + inlined from 'betaDistribution::betaDistribution(double, double, int, discretizationType)' at betaDistribution.cpp:36:19: +betaDistribution.cpp:72:26: warning: '*this.betaDistribution::_alpha' is used uninitialized [-Wuninitialized] + 72 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories())) + | ^~~~~~ +betaDistribution.cpp:72:49: warning: '*this.betaDistribution::_beta' may be used uninitialized [-Wmaybe-uninitialized] + 72 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories())) + | ^~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp @@ -709,35 +753,10 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeJumps.o computeJumps.cpp -In member function 'virtual void betaDistribution::setBetaParameters(int, double, double)', - inlined from 'betaDistribution::betaDistribution(double, double, int, discretizationType)' at betaDistribution.cpp:36:19: -betaDistribution.cpp:72:26: warning: '*this.betaDistribution::_alpha' is used uninitialized [-Wuninitialized] - 72 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories())) - | ^~~~~~ -betaDistribution.cpp:72:49: warning: '*this.betaDistribution::_beta' may be used uninitialized [-Wmaybe-uninitialized] - 72 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories())) - | ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp -In file included from gammaDistributionPlusInvariant.h:9, - from gammaDistributionPlusInvariant.cpp:1: -distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' - 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from generalGammaDistributionPlusInvariant.h:9, from generalGammaDistributionPlusInvariant.cpp:1: distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] @@ -746,14 +765,9 @@ generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2codon.o bblEM2codon.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndK.o bestAlphaAndK.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp In file included from computeJumps.cpp:1: computeJumps.h: In constructor 'computeJumps::gFunc::gFunc(double, double, double)': computeJumps.h:59:25: warning: 'computeJumps::gFunc::_Lambda2' will be initialized after [-Wreorder] @@ -765,15 +779,29 @@ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] 256 | computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) | ^~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gtrModel.o gtrModel.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp +In file included from gammaDistributionPlusInvariant.h:9, + from gammaDistributionPlusInvariant.cpp:1: +distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' + 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)': seqeuncesFilter.cpp:141:25: warning: unused variable 'pAlph' [-Wunused-variable] 141 | const alphabet* pAlph = sc.getAlphabet(); | ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestGtrModelParams.o bestGtrModelParams.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o integerAlphabet.o integerAlphabet.cpp -In file included from optGammaMixtureEM.cpp:1: +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.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; + | ^~~~~~ +In file included from GamMixtureOptimizer.cpp:3: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': optGammaMixtureEM.h:76:25: warning: unused variable 'res1' [-Wunused-variable] 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); @@ -782,10 +810,6 @@ optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable] 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); | ^~~~~~~~ -suffStatGammaMixture.cpp: In member function 'void suffStatGammaMixture::computeStatistics()': -suffStatGammaMixture.cpp:123:33: warning: variable 'Exp_Rk' set but not used [-Wunused-but-set-variable] - 123 | MDOUBLE Exp_Rk, Exp_LogRk, sum; - | ^~~~~~ 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); @@ -805,7 +829,7 @@ suffStatGammaMixture.cpp:216:17: warning: variable 'res2' set but not used [-Wunused-but-set-variable] 216 | MDOUBLE res2 = 0.0; | ^~~~ -In file included from GamMixtureOptimizer.cpp:3: +In file included from optGammaMixtureEM.cpp:1: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': optGammaMixtureEM.h:76:25: warning: unused variable 'res1' [-Wunused-variable] 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); @@ -814,17 +838,6 @@ optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable] 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); | ^~~~~~~~ -In file included from seqeuncesFilter.h:6, - from seqeuncesFilter.cpp:1: -In member function 'const sequence& sequenceContainer::operator[](int) const', - inlined from 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)' at seqeuncesFilter.cpp:175:16: -sequenceContainer.h:31:88: warning: 'refID' may be used uninitialized [-Wmaybe-uninitialized] - 31 | const sequence& operator[](const int id) const {return _seqDataVec[_id2place[id]];} - | ^ -seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)': -seqeuncesFilter.cpp:165:13: note: 'refID' was declared here - 165 | int refID; - | ^~~~~ mixtureDistribution.cpp: In member function 'virtual const double mixtureDistribution::rates(int) const': mixtureDistribution.cpp:221:40: warning: 'componentNum' may be used uninitialized [-Wmaybe-uninitialized] 221 | return _components[componentNum]->rates(categoryInComponent) * _globalRate; @@ -854,28 +867,6 @@ mixtureDistribution.cpp:228:27: note: 'categoryInComponent' was declared here 228 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~~~~~~~~ -In file included from gtrModel.cpp:1: -gtrModel.h: In constructor 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)': -gtrModel.h:54:17: warning: 'gtrModel::_g2t' will be initialized after [-Wreorder] - 54 | MDOUBLE _g2t; - | ^~~~ -gtrModel.h:47:17: warning: 'Vdouble gtrModel::_freq' [-Wreorder] - 47 | Vdouble _freq; - | ^~~~~ -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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, @@ -929,6 +920,51 @@ mixtureDistribution.cpp:72:43: note: 'pComp' declared here 72 | generalGammaDistribution* pComp; | ^~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp +In file included from seqeuncesFilter.h:6, + from seqeuncesFilter.cpp:1: +In member function 'const sequence& sequenceContainer::operator[](int) const', + inlined from 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)' at seqeuncesFilter.cpp:175:16: +sequenceContainer.h:31:88: warning: 'refID' may be used uninitialized [-Wmaybe-uninitialized] + 31 | const sequence& operator[](const int id) const {return _seqDataVec[_id2place[id]];} + | ^ +seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)': +seqeuncesFilter.cpp:165:13: note: 'refID' was declared here + 165 | int refID; + | ^~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2codon.o bblEM2codon.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndK.o bestAlphaAndK.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gtrModel.o gtrModel.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestGtrModelParams.o bestGtrModelParams.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o integerAlphabet.o integerAlphabet.cpp +In file included from bestGtrModelParams.cpp:3: +bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': +bestGtrModelParams.h:175:28: 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, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from gtrModel.cpp:1: +gtrModel.h: In constructor 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)': +gtrModel.h:54:17: warning: 'gtrModel::_g2t' will be initialized after [-Wreorder] + 54 | MDOUBLE _g2t; + | ^~~~ +gtrModel.h:47:17: warning: 'Vdouble gtrModel::_freq' [-Wreorder] + 47 | Vdouble _freq; + | ^~~~~ +gtrModel.cpp:5:1: warning: when initialized here [-Wreorder] + 5 | gtrModel::gtrModel(const Vdouble& freq, + | ^~~~~~~~ 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; @@ -1147,12 +1183,12 @@ make[2]: Entering directory '/build/reproducible-path/fastml-3.11/programs' cd fastml && make all cd gainLoss && make all -cd indelCoder && make all make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' +cd indelCoder && make all making depend +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' making depend +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' making depend g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoder.o indelCoder.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp @@ -1160,6 +1196,17 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o character.o character.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.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(); + | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp @@ -1181,17 +1228,29 @@ character.cpp:17:13: note: 'longestGapStIndex' was declared here 17 | int longestGapStIndex; | ^~~~~~~~~~~~~~~~~ -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(); - | ^~~~~~~ +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 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) + | ^~~~~~~~~~~~~~~~~ character.cpp: In member function 'void character::checkForTriangleInequality(int, int)': character.cpp:6:70: warning: 'longestGapStIndex' may be used uninitialized [-Wmaybe-uninitialized] 6 | if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][longestGapStIndex]){ @@ -1199,6 +1258,55 @@ character.cpp:17:13: note: 'longestGapStIndex' was declared here 17 | int longestGapStIndex; | ^~~~~~~~~~~~~~~~~ +In file included from bbAlg.h:8, + from bbAlg.cpp:1: +bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': +bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] + 14 | const string& _reportFileName; + | ^~~~~~~~~~~~~~~ +bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] + 13 | const int _minNumOfNodesToVisit; + | ^~~~~~~~~~~~~~~~~~~~~ +bbReport.h:10:18: warning: when initialized here [-Wreorder] + 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) + | ^~~~~~~~~~~~~~~~~ +In file included from bbReport.cpp:1: +bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': +bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] + 14 | const string& _reportFileName; + | ^~~~~~~~~~~~~~~ +bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] + 13 | const int _minNumOfNodesToVisit; + | ^~~~~~~~~~~~~~~~~~~~~ +bbReport.h:10:18: warning: when initialized here [-Wreorder] + 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) + | ^~~~~~~~~~~~~~~~~ +In file included from 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, + | ^~~~~~~~~~~~~~~~~~~~ +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() { + | ^~~~~~~~~~~~~~~~~~~ +bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': +bbEvaluateSpecificAV.cpp:65:33: warning: unused variable 'rate' [-Wunused-variable] + 65 | MDOUBLE rate = _sp.rates(categor); // the r. + | ^~~~ +In file included from mainbb.h:4, + from fastml.cpp:1: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] + 62 | static const string usege_splash_screen() { + | ^~~~~~~~~~~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h: In constructor 'bb_options::bb_options(int&, char**)': bb_options.h:49:16: warning: 'bb_options::reportFile' will be initialized after [-Wreorder] @@ -1273,59 +1381,6 @@ 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) - | ^~~~~~~~~~~~~~~~~ -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. - | ^~~~ -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 bbAlg.h:8, - from bbAlg.cpp:1: -bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': -bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] - 14 | const string& _reportFileName; - | ^~~~~~~~~~~~~~~ -bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] - 13 | const int _minNumOfNodesToVisit; - | ^~~~~~~~~~~~~~~~~~~~~ -bbReport.h:10:18: warning: when initialized here [-Wreorder] - 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) - | ^~~~~~~~~~~~~~~~~ -In file included from 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, - | ^~~~~~~~~~~~~~ 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; @@ -1345,35 +1400,7 @@ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] 7 | bbAlg::bbAlg(const tree& et, | ^~~~~ -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; - | ^~~~ -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) - | ^~~~~~~~~~~~~~~~~ -computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': -computeMarginalReconstruction.cpp:67:25: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] - 67 | MDOUBLE likelihoodOfPos = 0; - | ^~~~~~~~~~~~~~~ -computeMarginalReconstruction.cpp:45:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] - 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from bbfindBestAVDynProg.h:5, - from bbfindBestAVDynProg.cpp:1: +bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ @@ -1382,6 +1409,19 @@ 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 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() { + | ^~~~~~~~~~~~~~~~~~~ +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; + | ^~~~ 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; @@ -1392,6 +1432,13 @@ bbReport.cpp:10:1: warning: when initialized here [-Wreorder] 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : | ^~~~~~~~~~~ +In file included from bbNodeOrderAlg.h:5, + from bbAlg.h:5: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] + 62 | static const string usege_splash_screen() { + | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp In file included from bbAlg.h:8, from mainbb.cpp:5: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': @@ -1404,17 +1451,22 @@ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ -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() { - | ^~~~~~~~~~~~~~~~~~~ -In file included from mainbb.h:4, - from fastml.cpp:1: -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp +computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': +computeMarginalReconstruction.cpp:67:25: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] + 67 | MDOUBLE likelihoodOfPos = 0; + | ^~~~~~~~~~~~~~~ +computeMarginalReconstruction.cpp:45:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] + 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp In file included from mainbb.cpp:31: ../../libs/phylogeny/bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': ../../libs/phylogeny/bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] @@ -1426,31 +1478,9 @@ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from bbNodeOrderAlg.h:5, - from bbAlg.h:5: -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp In file included from mainbb.h:4, from mainbb.cpp:1: bb_options.h: At global scope: @@ -1459,92 +1489,6 @@ | ^~~~~~~~~~~~~~~~~~~ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, - from gainLossUtils.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLossUtils.cpp:19: -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -../../libs/phylogeny/distributionPlusInvariant.h: At global scope: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -In file included from gainLossUtils.cpp:20: -../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' - 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, - from gainLossUtils.h:27, - from sankoffReconstructGL.h:29, - from sankoffReconstructGL.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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) - | ^ -gainLossUtils.cpp:88:27: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] - 88 | if(probs) - | ^ -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; - | ^~~~~~~~~~ -gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': -gainLossUtils.cpp:788:17: warning: unused variable 'scale' [-Wunused-variable] - 788 | MDOUBLE scale; - | ^~~~~ -In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, - from gainLossUtils.h:27, - from gainLossModel.h:27, - from optimizeGainLossModelVV.h:27, - from optimizeGainLossModelVV.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, - from gainLossUtils.h:27, from gainLossModel.h:27, from gainLossModel.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] @@ -1553,27 +1497,6 @@ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLoss.h:30, - from gainLossProject.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -In file included from gainLossUtils.h:27, - from gainLossModel.h:27, - from gainLoss.h:35: -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModelVV.h: In constructor 'optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)': -optimizeGainLossModelVV.h:82:18: warning: 'optimizeGainLossModelVV::_weightsUniqPatterns' will be initialized after [-Wreorder] - 82 | Vdouble* _weightsUniqPatterns; - | ^~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModelVV.h:81:27: warning: 'unObservableData* optimizeGainLossModelVV::_unObservableData_p' [-Wreorder] - 81 | unObservableData* _unObservableData_p; - | ^~~~~~~~~~~~~~~~~~~ -optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] - 25 | optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, - | ^~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -1618,58 +1541,18 @@ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): | ^~~~~~~~~~~~~ -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)': -sankoffReconstructGL.h:85:16: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] - 85 | string _outDir; - | ^~~~~~~ -sankoffReconstructGL.h:84:17: warning: 'double sankoffReconstructGL::_costMatrixGainLossRatio' [-Wreorder] - 84 | MDOUBLE _costMatrixGainLossRatio; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] - 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): - | ^~~~~~~~~~~~~~~~~~~~ -sankoffReconstructGL.h:84:17: warning: 'sankoffReconstructGL::_costMatrixGainLossRatio' will be initialized after [-Wreorder] - 84 | MDOUBLE _costMatrixGainLossRatio; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -sankoffReconstructGL.h:83:17: warning: 'double sankoffReconstructGL::_distanceFromRootForRecent' [-Wreorder] - 83 | MDOUBLE _distanceFromRootForRecent; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] - 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): - | ^~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModelVV.cpp:258:41: warning: unused variable 'currentlogL' [-Wunused-variable] - 258 | MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); - | ^~~~~~~~~~~ -In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, - from gainLossUtils.h:27, - from gainLossModel.h:27, - from optimizeGainLossModel.h:27, - from optimizeGainLossModel.cpp:17: +In file included from gainLoss.h:30, + from gainLossOptimizer.h:24, + from gainLossOptimizer.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ +In file included from gainLossUtils.h:27, + from gainLossModel.h:27, + from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModelVV.cpp:76:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] - 76 | MDOUBLE sumPijQij; - | ^~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -1688,144 +1571,22 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, - from bblLS.h:27, - from bblLS.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLoss.h:30, - from gainLossOptimizer.h:24, - from gainLossOptimizer.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -In file included from gainLossUtils.h:27, - from gainLossModel.h:27, - from gainLoss.h:35: -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModel.h: In constructor 'optimizeGainLossModel::optimizeGainLossModel(const tree&, stochasticProcess&, const sequenceContainer&, bool, double, int, Vdouble*, unObservableData*)': -optimizeGainLossModel.h:87:18: warning: 'optimizeGainLossModel::_weightsUniqPatterns' will be initialized after [-Wreorder] - 87 | Vdouble* _weightsUniqPatterns; - | ^~~~~~~~~~~~~~~~~~~~ -optimizeGainLossModel.h:86:27: warning: 'unObservableData* optimizeGainLossModel::_unObservableData_p' [-Wreorder] - 86 | unObservableData* _unObservableData_p; - | ^~~~~~~~~~~~~~~~~~~ -optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] - 20 | optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, - | ^~~~~~~~~~~~~~~~~~~~~ -bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] - 50 | MDOUBLE curL =NULL); - | ^~~~ -bblLS.h:58:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] - 58 | MDOUBLE curL =NULL); - | ^~~~ -bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': -bblLS.h:119:27: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] - 119 | unObservableData* _unObservableData_p; - | ^~~~~~~~~~~~~~~~~~~ -bblLS.h:118:18: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] - 118 | Vdouble* _weights; - | ^~~~~~~~ -bblLS.h:96:18: warning: when initialized here [-Wreorder] - 96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, - | ^~~~~~~~~~~~~~ -bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': -bblLS.h:174:27: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] - 174 | unObservableData* _unObservableData_p; - | ^~~~~~~~~~~~~~~~~~~ -bblLS.h:173:18: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] - 173 | Vdouble* _weights; - | ^~~~~~~~ -bblLS.h:152:18: warning: when initialized here [-Wreorder] - 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLoss.h:30, - from computeCorrelations.h:25, - from computeCorrelations.cpp:17: + from gainLossUtils.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ -In file included from gainLossUtils.h:27, - from gainLossModel.h:27, - from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLoss.h:30, - from simulateChangesAlongTree.cpp:20: +In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, + from gainLossUtils.h:27, + from siteSpecificGL.cpp:23: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ -In file included from gainLossUtils.h:27, - from gainLossModel.h:27, - from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, stochasticProcess*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': -bblLS.cpp:36:21: warning: NULL used in arithmetic [-Wpointer-arith] - 36 | if (curL == NULL) - | ^~~~ -optimizeGainLossModel.cpp:85:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] - 85 | MDOUBLE sumPijQij; - | ^~~~~~~~~ -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, std::vector >&, const distribution*, const distribution*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': -bblLS.cpp:112:21: warning: NULL used in arithmetic [-Wpointer-arith] - 112 | if (curL == NULL) - | ^~~~ 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] @@ -1910,35 +1671,17 @@ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, | ^~~~~~~~~~~~~~~~~ -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 - | ^~~~~~~~~~~~~ -In file included from gainLoss.h:30, - from rate4siteGL.h:24, - from rate4siteGL.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -In file included from gainLossUtils.h:27, - from gainLossModel.h:27, - from gainLoss.h:35: -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, - from siteSpecificGL.cpp:23: + from gainLossModel.h:27, + from optimizeGainLossModelVV.h:27, + from optimizeGainLossModelVV.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': -computeCorrelations.cpp:408:29: warning: unused variable 'isHigherNminReducedFreqOfHighCorr' [-Wunused-variable] - 408 | int isHigherNminReducedFreqOfHighCorr = false; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -1955,45 +1698,82 @@ 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:348:21: warning: unused variable 'typeIndex' [-Wunused-variable] - 348 | int typeIndex = corIndex % _EventTypes.size(); // in case both Spearman and pearson are used - | ^~~~~~~~~ -computeCorrelations.cpp: In member function 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)': -computeCorrelations.cpp:559:30: warning: NULL used in arithmetic [-Wpointer-arith] - 559 | if(!simCorrelStream==NULL) - | ^~~~ -computeCorrelations.cpp:569:38: warning: NULL used in arithmetic [-Wpointer-arith] - 569 | if(!simCorrelStream==NULL) - | ^~~~ -computeCorrelations.cpp:579:38: warning: NULL used in arithmetic [-Wpointer-arith] - 579 | if(!simCorrelStream==NULL) - | ^~~~ -computeCorrelations.cpp:584:30: warning: NULL used in arithmetic [-Wpointer-arith] - 584 | if(!simCorrelStream==NULL) - | ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp +optimizeGainLossModelVV.h: In constructor 'optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)': +optimizeGainLossModelVV.h:82:18: warning: 'optimizeGainLossModelVV::_weightsUniqPatterns' will be initialized after [-Wreorder] + 82 | Vdouble* _weightsUniqPatterns; + | ^~~~~~~~~~~~~~~~~~~~ +optimizeGainLossModelVV.h:81:27: warning: 'unObservableData* optimizeGainLossModelVV::_unObservableData_p' [-Wreorder] + 81 | unObservableData* _unObservableData_p; + | ^~~~~~~~~~~~~~~~~~~ +optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] + 25 | optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from gainLossUtils.cpp:19: +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +../../libs/phylogeny/distributionPlusInvariant.h: At global scope: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +In file included from gainLossUtils.cpp:20: +../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' + 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +optimizeGainLossModelVV.cpp:258:41: warning: unused variable 'currentlogL' [-Wunused-variable] + 258 | MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); + | ^~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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) + | ^ gainLossOptimizer.cpp:543:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] 543 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossUtils.cpp:88:27: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + 88 | if(probs) + | ^ gainLossOptimizer.cpp:487:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] 487 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -computeCorrelations.cpp: In member function 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)': -computeCorrelations.cpp:676:37: warning: variable 'prevNumberOfSimulationsInRange' set but not used [-Wunused-but-set-variable] - 676 | int prevNumberOfSimulationsInRange = 1; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -computeCorrelations.cpp:677:37: warning: variable 'prevNumberOfSimulationPointsMoreExtremeOrEqToCorr' set but not used [-Wunused-but-set-variable] - 677 | int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -computeCorrelations.cpp:679:37: warning: unused variable 'numOfBinsWithLowerSignificance' [-Wunused-variable] - 679 | int numOfBinsWithLowerSignificance = 0; // allow 2 "bin-iteration" even with lower significance to mitigate chance of "missing" higher significance in lower bin - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -computeCorrelations.cpp:680:38: warning: unused variable 'isNextLowerBinAllowed' [-Wunused-variable] - 680 | bool isNextLowerBinAllowed = true; - | ^~~~~~~~~~~~~~~~~~~~~ +In file included from siteSpecificGL.cpp:24: +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +optimizeGainLossModelVV.cpp:76:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] + 76 | MDOUBLE sumPijQij; + | ^~~~~~~~~ gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengthsvv(int)': gainLossOptimizer.cpp:634:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] 634 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); @@ -2001,21 +1781,22 @@ gainLossOptimizer.cpp:677:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] 677 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:623:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] - 623 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -computeCorrelations.cpp: In member function 'void computeCorrelations::produceSymeticMatrix(VVVdouble&, bool)': -computeCorrelations.cpp:894:26: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] - 894 | if(!numOfSites_A == numOfSites_B){ - | ^~ -computeCorrelations.cpp:894:12: note: add parentheses around left hand side expression to silence this warning - 894 | if(!numOfSites_A == numOfSites_B){ - | ^~~~~~~~~~~~~ - | ( ) -In file included from siteSpecificGL.cpp:24: +In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, + from gainLossUtils.h:27, + from gainLossModel.h:27, + from computePosteriorExpectationOfChange.cpp:25: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ +gainLossOptimizer.cpp:623:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] + 623 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2029,46 +1810,22 @@ 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; - | ^~~ -rate4siteGL.h:58:28: warning: 'stochasticProcess* rate4siteGL::_sp' [-Wreorder] - 58 | stochasticProcess *_sp; - | ^~~ -rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder] - 24 | rate4siteGL::rate4siteGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, unObservableData* unObservableData_p): - | ^~~~~~~~~~~ -computeCorrelations.cpp: In member function 'void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::string*)': -computeCorrelations.cpp:1009:14: warning: unused variable 'isPearson' [-Wunused-variable] - 1009 | bool isPearson = false; - | ^~~~~~~~~ -computeCorrelations.cpp:1025:13: warning: unused variable 'numOfbranches' [-Wunused-variable] - 1025 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node - | ^~~~~~~~~~~~~ -computeCorrelations.cpp: In member function 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)': -computeCorrelations.cpp:1347:67: warning: narrowing conversion of 'gainLossOptions::_pValueCutOffForBootStrap' from 'double' to 'float' [-Wnarrowing] - 1347 | float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001}; - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -rate4siteGL.cpp: In member function 'void rate4siteGL::printRatesBayes(std::ostream&, const Vdouble&)': -rate4siteGL.cpp:151:13: warning: unused variable 'precisionHigh' [-Wunused-variable] - 151 | int precisionHigh = 5; - | ^~~~~~~~~~~~~ -rate4siteGL.cpp:152:13: warning: unused variable 'precisionLow' [-Wunused-variable] - 152 | int precisionLow = 3; - | ^~~~~~~~~~~~ -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:30, - from gainLoss4site.h:24, - from gainLoss4site.cpp:17: +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; + | ^~~~~~~~~~ +gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': +gainLossUtils.cpp:788:17: warning: unused variable 'scale' [-Wunused-variable] + 788 | MDOUBLE scale; + | ^~~~~ +In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, + from gainLossUtils.h:27, + from gainLossModel.h:27, + from optimizeGainLossModel.h:27, + from optimizeGainLossModel.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ -In file included from gainLossUtils.h:27, - from gainLossModel.h:27, - from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2088,19 +1845,34 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, - from gainLossUtils.h:27, - from gainLossModel.h:27, - from computePosteriorExpectationOfChange.cpp:25: +optimizeGainLossModel.h: In constructor 'optimizeGainLossModel::optimizeGainLossModel(const tree&, stochasticProcess&, const sequenceContainer&, bool, double, int, Vdouble*, unObservableData*)': +optimizeGainLossModel.h:87:18: warning: 'optimizeGainLossModel::_weightsUniqPatterns' will be initialized after [-Wreorder] + 87 | Vdouble* _weightsUniqPatterns; + | ^~~~~~~~~~~~~~~~~~~~ +optimizeGainLossModel.h:86:27: warning: 'unObservableData* optimizeGainLossModel::_unObservableData_p' [-Wreorder] + 86 | unObservableData* _unObservableData_p; + | ^~~~~~~~~~~~~~~~~~~ +optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] + 20 | optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, + | ^~~~~~~~~~~~~~~~~~~~~ +optimizeGainLossModel.cpp:85:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] + 85 | MDOUBLE sumPijQij; + | ^~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp +In file included from gainLoss.h:30, + from rate4siteGL.h:24, + from rate4siteGL.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ +In file included from gainLossUtils.h:27, + from gainLossModel.h:27, + from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:30, - from computeCountsGL.h:24, - from computeCountsGL.cpp:17: + from gainLossProject.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ @@ -2153,17 +1925,6 @@ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLoss.h:30, - from simulateOnePos.cpp:32: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -In file included from gainLossUtils.h:27, - from gainLossModel.h:27, - from gainLoss.h:35: -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -2180,6 +1941,18 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from gainLoss.h:30, + from computeCountsGL.h:24, + from computeCountsGL.cpp:17: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +In file included from gainLossUtils.h:27, + from gainLossModel.h:27, + from gainLoss.h:35: +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -2196,61 +1969,48 @@ 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; +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; | ^~~ -gainLoss4site.h:61:45: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] - 61 | vector > _spVVec; //save stochasticProcess for each category - | ^~~~~~~ -gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] - 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, - | ^~~~~~~~~~~~~ -gainLoss4site.h:79:27: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] - 79 | unObservableData* _unObservableData_p; // +rate4siteGL.h:58:28: warning: 'stochasticProcess* rate4siteGL::_sp' [-Wreorder] + 58 | stochasticProcess *_sp; + | ^~~ +rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder] + 24 | rate4siteGL::rate4siteGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, unObservableData* unObservableData_p): + | ^~~~~~~~~~~ +rate4siteGL.cpp: In member function 'void rate4siteGL::printRatesBayes(std::ostream&, const Vdouble&)': +rate4siteGL.cpp:151:13: warning: unused variable 'precisionHigh' [-Wunused-variable] + 151 | int precisionHigh = 5; + | ^~~~~~~~~~~~~ +rate4siteGL.cpp:152:13: warning: unused variable 'precisionLow' [-Wunused-variable] + 152 | int precisionLow = 3; + | ^~~~~~~~~~~~ +../../libs/phylogeny/distributionPlusInvariant.h: At global scope: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +In file included from gainLoss.cpp:25: +../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' + 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from gainLoss.cpp:41: +bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] + 50 | MDOUBLE curL =NULL); + | ^~~~ +bblLS.h:58:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] + 58 | MDOUBLE curL =NULL); + | ^~~~ +bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': +bblLS.h:119:27: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] + 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ -gainLoss4site.h:78:17: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] - 78 | MDOUBLE _alphaConf; - | ^~~~~~~~~~ -gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] - 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, - | ^~~~~~~~~~~~~ -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] - 72 | bool _simulateNullModel; - | ^~~~~~~~~~~~~~~~~~ -simulateOnePos.h:63:13: warning: 'int simulateOnePos::_simNum' [-Wreorder] - 63 | int _simNum; - | ^~~~~~~ -simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] - 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile - | ^~~~~~~~~~~~~~ -simulateOnePos.h:65:17: warning: 'simulateOnePos::_theta' will be initialized after [-Wreorder] - 65 | MDOUBLE _theta; - | ^~~~~~ -simulateOnePos.h:64:17: warning: 'double simulateOnePos::_sumGainLoss' [-Wreorder] - 64 | MDOUBLE _sumGainLoss; - | ^~~~~~~~~~~~ -simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] - 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile - | ^~~~~~~~~~~~~~ -simulateOnePos.h:75:18: warning: 'simulateOnePos::_freq_cpN' will be initialized after [-Wreorder] - 75 | Vdouble* _freq_cpN; - | ^~~~~~~~~ -simulateOnePos.h:69:18: warning: 'std::ostream* simulateOnePos::_simulatedEvents' [-Wreorder] - 69 | ostream *_simulatedEvents; - | ^~~~~~~~~~~~~~~~ -simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] - 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile - | ^~~~~~~~~~~~~~ -simulateOnePos.cpp: In member function 'void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::string)': -simulateOnePos.cpp:181:30: warning: unused variable 'isRevers' [-Wunused-variable] - 181 | bool isRevers = false; - | ^~~~~~~~ -simulateOnePos.cpp:202:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] - 202 | MDOUBLE sumQii = 1.0; - | ^~~~~~ +bblLS.h:118:18: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] + 118 | Vdouble* _weights; + | ^~~~~~~~ +bblLS.h:96:18: warning: when initialized here [-Wreorder] + 96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, + | ^~~~~~~~~~~~~~ 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; @@ -2270,6 +2030,16 @@ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] 28 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, VVdouble& logLpostPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ +bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': +bblLS.h:174:27: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] + 174 | unObservableData* _unObservableData_p; + | ^~~~~~~~~~~~~~~~~~~ +bblLS.h:173:18: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] + 173 | Vdouble* _weights; + | ^~~~~~~~ +bblLS.h:152:18: warning: when initialized here [-Wreorder] + 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, std::vector >&, distribution*, distribution*, std::string&, VVVdouble&, double, bool)': computeCountsGL.h:109:23: warning: 'computeCountsGL::_lossDist' will be initialized after [-Wreorder] 109 | distribution* _lossDist; @@ -2289,41 +2059,6 @@ 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): | ^~~~~~~~~~~~~~~ -../../libs/phylogeny/distributionPlusInvariant.h: At global scope: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -In file included from gainLoss.cpp:25: -../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' - 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLoss.cpp:41: -bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] - 50 | MDOUBLE curL =NULL); - | ^~~~ -bblLS.h:58:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] - 58 | MDOUBLE curL =NULL); - | ^~~~ -bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': -bblLS.h:119:27: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] - 119 | unObservableData* _unObservableData_p; - | ^~~~~~~~~~~~~~~~~~~ -bblLS.h:118:18: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] - 118 | Vdouble* _weights; - | ^~~~~~~~ -bblLS.h:96:18: warning: when initialized here [-Wreorder] - 96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, - | ^~~~~~~~~~~~~~ -bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': -bblLS.h:174:27: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] - 174 | unObservableData* _unObservableData_p; - | ^~~~~~~~~~~~~~~~~~~ -bblLS.h:173:18: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] - 173 | Vdouble* _weights; - | ^~~~~~~~ -bblLS.h:152:18: warning: when initialized here [-Wreorder] - 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.h: In constructor 'gainLoss::gainLoss()': gainLoss.h:266:28: warning: 'gainLoss::_unObservableData_p' will be initialized after [-Wreorder] 266 | unObservableData* _unObservableData_p; @@ -2352,13 +2087,6 @@ 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) | ^~~~~~~~ -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 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)': gainLoss.cpp:604:14: warning: unused variable 'missigDataChar' [-Wunused-variable] 604 | char missigDataChar = -2; @@ -2371,21 +2099,121 @@ 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ | ^~~~~~~~~~~~~~~~~~~ | ( ) +In file included from gainLoss.h:30, + from computeCorrelations.h:25, + from computeCorrelations.cpp:17: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +In file included from gainLossUtils.h:27, + from gainLossModel.h:27, + from gainLoss.h:35: +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': gainLoss.cpp:1868:25: warning: unused variable 'sumPijQij' [-Wunused-variable] 1868 | MDOUBLE sumPijQij = normalizeQ(sp); | ^~~~~~~~~ -gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': -gainLossUtils.cpp:312:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] - 312 | return res; - | ^~~ -gainLossUtils.cpp:285:17: note: 'res' was declared here - 285 | MDOUBLE res; - | ^~~ +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp +In file included from gainLoss.h:30, + from gainLoss4site.h:24, + from gainLoss4site.cpp:17: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +In file included from gainLossUtils.h:27, + from gainLossModel.h:27, + from gainLoss.h:35: +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::string&, unObservableData*, double)': +gainLoss4site.h:68:14: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] + 68 | tree _tr; + | ^~~ +gainLoss4site.h:61:45: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] + 61 | vector > _spVVec; //save stochasticProcess for each category + | ^~~~~~~ +gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] + 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, + | ^~~~~~~~~~~~~ +gainLoss4site.h:79:27: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] + 79 | unObservableData* _unObservableData_p; // + | ^~~~~~~~~~~~~~~~~~~ +gainLoss4site.h:78:17: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] + 78 | MDOUBLE _alphaConf; + | ^~~~~~~~~~ +gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] + 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, + | ^~~~~~~~~~~~~ +computeCorrelations.cpp: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)': +computeCorrelations.cpp:130:13: warning: unused variable 'numOfbranches' [-Wunused-variable] + 130 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node + | ^~~~~~~~~~~~~ +computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': +computeCorrelations.cpp:408:29: warning: unused variable 'isHigherNminReducedFreqOfHighCorr' [-Wunused-variable] + 408 | int isHigherNminReducedFreqOfHighCorr = false; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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; + | ^~~~~~~~~ +computeCorrelations.cpp:348:21: warning: unused variable 'typeIndex' [-Wunused-variable] + 348 | int typeIndex = corIndex % _EventTypes.size(); // in case both Spearman and pearson are used + | ^~~~~~~~~ +computeCorrelations.cpp: In member function 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)': +computeCorrelations.cpp:559:30: warning: NULL used in arithmetic [-Wpointer-arith] + 559 | if(!simCorrelStream==NULL) + | ^~~~ +computeCorrelations.cpp:569:38: warning: NULL used in arithmetic [-Wpointer-arith] + 569 | if(!simCorrelStream==NULL) + | ^~~~ +computeCorrelations.cpp:579:38: warning: NULL used in arithmetic [-Wpointer-arith] + 579 | if(!simCorrelStream==NULL) + | ^~~~ +computeCorrelations.cpp:584:30: warning: NULL used in arithmetic [-Wpointer-arith] + 584 | if(!simCorrelStream==NULL) + | ^~~~ 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; @@ -2402,17 +2230,46 @@ 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ | ^~~~~~~~~~~ | ( ) +computeCorrelations.cpp: In member function 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)': +computeCorrelations.cpp:676:37: warning: variable 'prevNumberOfSimulationsInRange' set but not used [-Wunused-but-set-variable] + 676 | int prevNumberOfSimulationsInRange = 1; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +computeCorrelations.cpp:677:37: warning: variable 'prevNumberOfSimulationPointsMoreExtremeOrEqToCorr' set but not used [-Wunused-but-set-variable] + 677 | int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +computeCorrelations.cpp:679:37: warning: unused variable 'numOfBinsWithLowerSignificance' [-Wunused-variable] + 679 | int numOfBinsWithLowerSignificance = 0; // allow 2 "bin-iteration" even with lower significance to mitigate chance of "missing" higher significance in lower bin + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +computeCorrelations.cpp:680:38: warning: unused variable 'isNextLowerBinAllowed' [-Wunused-variable] + 680 | bool isNextLowerBinAllowed = true; + | ^~~~~~~~~~~~~~~~~~~~~ +computeCorrelations.cpp: In member function 'void computeCorrelations::produceSymeticMatrix(VVVdouble&, bool)': +computeCorrelations.cpp:894:26: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] + 894 | if(!numOfSites_A == numOfSites_B){ + | ^~ +computeCorrelations.cpp:894:12: note: add parentheses around left hand side expression to silence this warning + 894 | if(!numOfSites_A == numOfSites_B){ + | ^~~~~~~~~~~~~ + | ( ) +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.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; | ^~~~~~ -gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const std::string&)': -gainLossOptions.cpp:2111:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] - 2111 | return returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp:2098:24: note: 'returnType' was declared here - 2098 | costMatrixType returnType; - | ^~~~~~~~~~ +computeCorrelations.cpp: In member function 'void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::string*)': +computeCorrelations.cpp:1009:14: warning: unused variable 'isPearson' [-Wunused-variable] + 1009 | bool isPearson = false; + | ^~~~~~~~~ +computeCorrelations.cpp:1025:13: warning: unused variable 'numOfbranches' [-Wunused-variable] + 1025 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node + | ^~~~~~~~~~~~~ +computeCorrelations.cpp: In member function 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)': +computeCorrelations.cpp:1347:67: warning: narrowing conversion of 'gainLossOptions::_pValueCutOffForBootStrap' from 'double' to 'float' [-Wnarrowing] + 1347 | float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001}; + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +computeCorrelations.cpp:1300:14: warning: variable 'it_siteB' set but not used [-Wunused-but-set-variable] + 1300 | it_B it_siteB = it_siteA->second.begin(); + | ^~~~~~~~ In file included from /usr/include/c++/14/iostream:41, from ../../libs/phylogeny/readTree.h:6, from ../../libs/phylogeny/tree.h:7, @@ -2447,6 +2304,192 @@ computePosteriorExpectationOfChange.cpp:216:17: note: 'pij' was declared here 216 | MDOUBLE pij; | ^~~ +gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': +gainLossUtils.cpp:312:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] + 312 | return res; + | ^~~ +gainLossUtils.cpp:285:17: note: 'res' was declared here + 285 | MDOUBLE res; + | ^~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp +gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const std::string&)': +gainLossOptions.cpp:2111:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] + 2111 | return returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp:2098:24: note: 'returnType' was declared here + 2098 | costMatrixType returnType; + | ^~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp +In file included from gainLoss.h:30, + from simulateChangesAlongTree.cpp:20: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +In file included from gainLossUtils.h:27, + from gainLossModel.h:27, + from gainLoss.h:35: +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from gainLoss.h:30, + from simulateOnePos.cpp:32: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +In file included from gainLossUtils.h:27, + from gainLossModel.h:27, + from gainLoss.h:35: +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from 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] + 72 | bool _simulateNullModel; + | ^~~~~~~~~~~~~~~~~~ +simulateOnePos.h:63:13: warning: 'int simulateOnePos::_simNum' [-Wreorder] + 63 | int _simNum; + | ^~~~~~~ +simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] + 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile + | ^~~~~~~~~~~~~~ +simulateOnePos.h:65:17: warning: 'simulateOnePos::_theta' will be initialized after [-Wreorder] + 65 | MDOUBLE _theta; + | ^~~~~~ +simulateOnePos.h:64:17: warning: 'double simulateOnePos::_sumGainLoss' [-Wreorder] + 64 | MDOUBLE _sumGainLoss; + | ^~~~~~~~~~~~ +simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] + 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile + | ^~~~~~~~~~~~~~ +simulateOnePos.h:75:18: warning: 'simulateOnePos::_freq_cpN' will be initialized after [-Wreorder] + 75 | Vdouble* _freq_cpN; + | ^~~~~~~~~ +simulateOnePos.h:69:18: warning: 'std::ostream* simulateOnePos::_simulatedEvents' [-Wreorder] + 69 | ostream *_simulatedEvents; + | ^~~~~~~~~~~~~~~~ +simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] + 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile + | ^~~~~~~~~~~~~~ +simulateOnePos.cpp: In member function 'void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::string)': +simulateOnePos.cpp:181:30: warning: unused variable 'isRevers' [-Wunused-variable] + 181 | bool isRevers = false; + | ^~~~~~~~ +simulateOnePos.cpp:202:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] + 202 | MDOUBLE sumQii = 1.0; + | ^~~~~~ +In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, + from gainLossUtils.h:27, + from bblLS.h:27, + from bblLS.cpp:17: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] + 50 | MDOUBLE curL =NULL); + | ^~~~ +bblLS.h:58:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] + 58 | MDOUBLE curL =NULL); + | ^~~~ +bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': +bblLS.h:119:27: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] + 119 | unObservableData* _unObservableData_p; + | ^~~~~~~~~~~~~~~~~~~ +bblLS.h:118:18: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] + 118 | Vdouble* _weights; + | ^~~~~~~~ +bblLS.h:96:18: warning: when initialized here [-Wreorder] + 96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, + | ^~~~~~~~~~~~~~ +bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': +bblLS.h:174:27: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] + 174 | unObservableData* _unObservableData_p; + | ^~~~~~~~~~~~~~~~~~~ +bblLS.h:173:18: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] + 173 | Vdouble* _weights; + | ^~~~~~~~ +bblLS.h:152:18: warning: when initialized here [-Wreorder] + 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, stochasticProcess*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': +bblLS.cpp:36:21: warning: NULL used in arithmetic [-Wpointer-arith] + 36 | if (curL == NULL) + | ^~~~ +bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, std::vector >&, const distribution*, const distribution*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': +bblLS.cpp:112:21: warning: NULL used in arithmetic [-Wpointer-arith] + 112 | if (curL == NULL) + | ^~~~ +In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, + from gainLossUtils.h:27, + from sankoffReconstructGL.h:29, + from sankoffReconstructGL.cpp:17: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)': +sankoffReconstructGL.h:85:16: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] + 85 | string _outDir; + | ^~~~~~~ +sankoffReconstructGL.h:84:17: warning: 'double sankoffReconstructGL::_costMatrixGainLossRatio' [-Wreorder] + 84 | MDOUBLE _costMatrixGainLossRatio; + | ^~~~~~~~~~~~~~~~~~~~~~~~ +sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] + 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): + | ^~~~~~~~~~~~~~~~~~~~ +sankoffReconstructGL.h:84:17: warning: 'sankoffReconstructGL::_costMatrixGainLossRatio' will be initialized after [-Wreorder] + 84 | MDOUBLE _costMatrixGainLossRatio; + | ^~~~~~~~~~~~~~~~~~~~~~~~ +sankoffReconstructGL.h:83:17: warning: 'double sankoffReconstructGL::_distanceFromRootForRecent' [-Wreorder] + 83 | MDOUBLE _distanceFromRootForRecent; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] + 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): + | ^~~~~~~~~~~~~~~~~~~~ +mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': +mainbb.cpp:428:108: warning: 'bm' may be used uninitialized [-Wmaybe-uninitialized] + 428 | bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); + | ^ +mainbb.cpp:423:28: note: 'bm' was declared here + 423 | bbAlg::boundMethod bm; + | ^~ ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o ar: creating libindelCoder.a a - indelCoder.o @@ -2457,13 +2500,6 @@ a - gaps.o ranlib libindelCoder.a g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder -mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': -mainbb.cpp:428:108: warning: 'bm' may be used uninitialized [-Wmaybe-uninitialized] - 428 | bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); - | ^ -mainbb.cpp:423:28: note: 'bm' was declared here - 423 | bbAlg::boundMethod bm; - | ^~ make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' 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] @@ -2580,13 +2616,6 @@ gainLoss.cpp:3852:37: note: 'Theta' was declared here 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; | ^~~~~ -computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': -computeCorrelations.cpp:505:33: warning: 'expextedFreq' may be used uninitialized [-Wmaybe-uninitialized] - 505 | if(freqOfHighCorr>expextedFreq && freqOfHighCorrexpextedFreq && freqOfHighCorr doubleRep.out.tmp -diff doubleRep.out.tmp doubleRep.out.standard -./split_test > split_test.out.tmp -diff split_test.out.tmp split_test.out.standard ./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp diff readTreeWithComments.out.tmp readTreeWithComments.out.standard +./split_test > split_test.out.tmp +diff split_test.out.tmp split_test.out.standard ./splitMap_test > splitMap_test.out.tmp +./doubleRep > doubleRep.out.tmp diff splitMap_test.out.tmp splitMap_test.out.standard -./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp -diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard -./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp -diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard +diff doubleRep.out.tmp doubleRep.out.standard ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard ./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard +./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp +diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard ./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp +./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard +diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny/tests' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/libs' @@ -2715,7 +2751,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/fastml/ - make -j42 install DESTDIR=/build/reproducible-path/fastml-3.11/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j20 install DESTDIR=/build/reproducible-path/fastml-3.11/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make all make[2]: Entering directory '/build/reproducible-path/fastml-3.11/libs' @@ -2729,12 +2765,12 @@ cd fastml && make install cd gainLoss && make install cd indelCoder && make install -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' -mkdir -p ../../bin make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' mkdir -p ../../bin -cp indelCoder ../../bin/indelCoder +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' +mkdir -p ../../bin cp fastml ../../bin/fastml +cp indelCoder ../../bin/indelCoder make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss @@ -2770,12 +2806,14 @@ 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/3842789/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3842789/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/2206049 and its subdirectories -I: Current time: Sat Apr 4 12:21:51 -12 2026 -I: pbuilder-time-stamp: 1775348511 +I: removing directory /srv/workspace/pbuilder/3842789 and its subdirectories +I: Current time: Mon Mar 3 08:03:10 +14 2025 +I: pbuilder-time-stamp: 1740938590