Diff of the two buildlogs: -- --- b1/build.log 2025-03-02 12:46:34.832745734 +0000 +++ b2/build.log 2025-03-02 12:48:35.335276034 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Mar 2 00:40:40 -12 2025 -I: pbuilder-time-stamp: 1740919240 +I: Current time: Sun Apr 5 09:09:36 +14 2026 +I: pbuilder-time-stamp: 1775329776 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/3550313/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1690579/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Apr 4 19:09 /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/1690579/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1690579/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=20 ' - DISTRIBUTION='unstable' - 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=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='97204711d1734456ae18dc53876f6b12' - 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='3550313' - PS1='# ' - PS2='> ' + INVOCATION_ID=453ebfda71c84ed6a190a8c5169661f6 + 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=1690579 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.sW962sjH/pbuilderrc_vfz7 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sW962sjH/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://46.16.76.132:3128' + 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.sW962sjH/pbuilderrc_zGKg --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sW962sjH/b2 --logfile b2/build.log fastml_3.11-4.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3550313/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1690579/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 unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] -Fetched 20.6 MB in 6s (3559 kB/s) +Fetched 20.6 MB in 2s (12.1 MB/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 ... 19778 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/1690579/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1690579/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 -j20 clean + make -j42 clean make[2]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make clean cd programs;make clean @@ -301,16 +337,16 @@ 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/libs/phylogeny' +make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' +rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o -make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' +make[4]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.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]: 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[4]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' -make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/libs' make[2]: Leaving directory '/build/reproducible-path/fastml-3.11' @@ -328,7 +364,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j20 "INSTALL=install --strip-program=true" + make -j42 "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' @@ -358,20 +394,6 @@ 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 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 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 -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 computeCounts.o computeCounts.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 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 @@ -386,6 +408,18 @@ 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] @@ -406,13 +440,25 @@ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 15 | computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/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 +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 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 In file included from /usr/include/c++/14/iostream:41, from readTree.h:6, from tree.h:7, @@ -445,9 +491,22 @@ 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 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 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 +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 likeDistfixRoot.o likeDistfixRoot.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: @@ -478,40 +537,10 @@ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:35: note: 'pij' was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 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 -goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)': -goldmanYangModel.cpp:8:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] - 8 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV): - | ^~~~~~~~~~~~~~~~ -goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, const Vdouble&, bool)': -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 likelihoodComputationFactors.o likelihoodComputationFactors.cpp In file included from generalGammaDistributionPlusInvariant.h:9, from simulateWithDependence.h:35, from simulateWithDependence.cpp:1: @@ -521,10 +550,28 @@ 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 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 +goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)': +goldmanYangModel.cpp:8:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] + 8 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV): + | ^~~~~~~~~~~~~~~~ +goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, const Vdouble&, bool)': +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 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 +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 +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 readTree.o readTree.cpp likeDist.cpp: In instantiation of 'double myNRmethod(double, double, double, regF, dF, double, int, int&) [with regF = C_evalLikeDist_d; dF = C_evalLikeDist_d2]': likeDist.cpp:269:22: required from here 269 | dist = myNRmethod(ax,bx,cx, @@ -542,6 +589,14 @@ likeDist.cpp:210:13: warning: variable 'oldIntervalSize' set but not used [-Wunused-but-set-variable] 210 | MDOUBLE oldIntervalSize = currentIntervalSize; | ^~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o recognizeFormat.o recognizeFormat.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 pijAccelerator.o pijAccelerator.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readTree.o readTree.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 recognizeFormat.o recognizeFormat.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModel.o replacementModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o searchStatus.o searchStatus.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 seqContainerTreeMap.o seqContainerTreeMap.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 sequence.o sequence.cpp @@ -583,13 +613,22 @@ 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 siteSpecificRate.o siteSpecificRate.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 someUtil.o someUtil.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 split.o split.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; - | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/cassert:44, + from njConstrain.cpp:4: +njConstrain.cpp: In function 'tree::TreeNode* joinNodesToSubtree(tree&, tree::TreeNode*&, tree::TreeNode*&)': +njConstrain.cpp:92:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 92 | assert (k=fatherNode->getNumberOfSons()+2); // both s1 and s2 should have been skiped + | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 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; @@ -610,22 +649,22 @@ 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 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 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 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 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 +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 doubleRep.o doubleRep.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 logRep.o logRep.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 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 +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 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()) @@ -633,8 +672,6 @@ 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 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 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(); @@ -642,15 +679,24 @@ 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 doubleRep.o doubleRep.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 logRep.o logRep.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 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 -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 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 +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 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 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] @@ -662,9 +708,7 @@ 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 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 likelihoodComputation2USSRV.o likelihoodComputation2USSRV.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=] @@ -673,14 +717,6 @@ 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 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 @@ -697,14 +733,6 @@ | ^~~~~~~~~~~~~~~~ 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 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 -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 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 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 @@ -716,16 +744,19 @@ 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 gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.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 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 +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 computeJumps.o computeJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.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 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 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=] @@ -734,9 +765,6 @@ 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 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 @@ -744,7 +772,30 @@ 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 +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 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 +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 gtrModel.o gtrModel.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 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] @@ -756,11 +807,8 @@ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] 256 | computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) | ^~~~~~~~~~~~ -seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)': -seqeuncesFilter.cpp:141:25: warning: unused variable 'pAlph' [-Wunused-variable] - 141 | const alphabet* pAlph = sc.getAlphabet(); - | ^~~~~ -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 +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 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; @@ -802,8 +850,6 @@ 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))); | ^~~~~~~~ -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 In file included from seqeuncesFilter.h:6, from seqeuncesFilter.cpp:1: In member function 'const sequence& sequenceContainer::operator[](int) const', @@ -815,8 +861,6 @@ 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 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 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; @@ -846,7 +890,28 @@ mixtureDistribution.cpp:228:27: note: 'categoryInComponent' was declared here 228 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp +In file included from gtrModel.cpp:1: +gtrModel.h: In constructor 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)': +gtrModel.h:54:17: 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, @@ -900,35 +965,6 @@ mixtureDistribution.cpp:72:43: note: 'pComp' declared here 72 | generalGammaDistribution* pComp; | ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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; @@ -1148,11 +1184,11 @@ cd fastml && make all cd gainLoss && make all cd indelCoder && make all -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' +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' making depend making depend -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' 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 @@ -1160,24 +1196,6 @@ 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. -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 -character.cpp: In member function 'int character::getLongestGapStIndex()': -character.cpp:28:16: warning: 'longestGapStIndex' may be used uninitialized [-Wmaybe-uninitialized] - 28 | return longestGapStIndex; - | ^~~~~~~~~~~~~~~~~ -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(); - | ^~~~~~~ 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 @@ -1192,6 +1210,24 @@ 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 mainbb.o mainbb.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp +indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': +indelCoder.cpp:422:13: warning: unused variable 'gapNum' [-Wunused-variable] + 422 | int gapNum = 1; + | ^~~~~~ +character.cpp: In member function 'int character::getLongestGapStIndex()': +character.cpp:28:16: warning: 'longestGapStIndex' may be used uninitialized [-Wmaybe-uninitialized] + 28 | return longestGapStIndex; + | ^~~~~~~~~~~~~~~~~ +character.cpp:17:13: note: 'longestGapStIndex' was declared here + 17 | int longestGapStIndex; + | ^~~~~~~~~~~~~~~~~ +indelCoder.cpp: In member function 'void indelCoder::printIndelSummary()': +indelCoder.cpp:587:14: warning: unused variable 'isSIC' [-Wunused-variable] + 587 | bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; + | ^~~~~ +indelCoder.cpp:597:13: warning: unused variable 'seqLeng' [-Wunused-variable] + 597 | int seqLeng = _sc.seqLen(); + | ^~~~~~~ character.cpp: In member function '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]){ @@ -1273,10 +1309,6 @@ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ In file included from 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] @@ -1288,6 +1320,17 @@ 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, + | ^~~~~~~~~~~~~~ In file included from bbAlg.h:8, from bbAlg.cpp:1: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': @@ -1300,37 +1343,10 @@ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ -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) - | ^~~~~~~~~~~~~~~~~ -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 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, - | ^~~~~~~~~~~~~~ +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 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] @@ -1370,6 +1386,26 @@ 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; + | ^~~~ +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; @@ -1377,6 +1413,11 @@ computeMarginalReconstruction.cpp:45:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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() { + | ^~~~~~~~~~~~~~~~~~~ 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; @@ -1387,12 +1428,6 @@ bbReport.cpp:10:1: warning: when initialized here [-Wreorder] 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : | ^~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 In file included from bbAlg.h:8, from mainbb.cpp:5: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': @@ -1416,11 +1451,6 @@ bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ -In file included from bbNodeOrderAlg.h:5: -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.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] @@ -1432,43 +1462,49 @@ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp 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: 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 ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, - from gainLossUtils.h:27, - from gainLossUtils.cpp:17: +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); | ^~~~~~~~ -../../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, +In file included 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); - | ^~~~~~~~ + 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 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); | ^~~~~~~~ @@ -1485,22 +1521,63 @@ 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: +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.cpp:20: -../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' - 19 | class gammaDistributionPlusInvariant : 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) - | ^ -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 +../../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 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 ../../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); + | ^~~~~~~~ +bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] + 50 | MDOUBLE curL =NULL); + | ^~~~ +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 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); | ^~~~~~~~ @@ -1517,17 +1594,6 @@ 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 optimizeGainLossModel.h:27, - from optimizeGainLossModel.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -1544,20 +1610,6 @@ 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.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, - | ^~~~~~~~~~~~~~~~~~~~~~~ -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; - | ^~~~~~~~~~ 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; @@ -1568,22 +1620,19 @@ optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] 20 | optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, | ^~~~~~~~~~~~~~~~~~~~~ -gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': -gainLossUtils.cpp:788:17: warning: unused variable 'scale' [-Wunused-variable] - 788 | MDOUBLE scale; - | ^~~~~ -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 -optimizeGainLossModelVV.cpp:258:41: warning: unused variable 'currentlogL' [-Wunused-variable] - 258 | MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); - | ^~~~~~~~~~~ +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) + | ^~~~ optimizeGainLossModel.cpp:85:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] 85 | MDOUBLE sumPijQij; | ^~~~~~~~~ -optimizeGainLossModelVV.cpp:76:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] - 76 | MDOUBLE sumPijQij; - | ^~~~~~~~~ In file included from gainLoss.h:30, - from gainLoss.cpp:20: + 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); | ^~~~~~~~ @@ -1593,6 +1642,44 @@ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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; + | ^~~ +computeCountsGL.h:102:28: warning: 'stochasticProcess* computeCountsGL::_sp' [-Wreorder] + 102 | stochasticProcess *_sp; + | ^~~ +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): + | ^~~~~~~~~~~~~~~ +computeCountsGL.h:117:17: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] + 117 | MDOUBLE _distanceFromNearestOTUForRecent; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +computeCountsGL.h:113:14: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] + 113 | bool _isSilent; + | ^~~~~~~~~ +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): + | ^~~~~~~~~~~~~~~ +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; + | ^~~~~~~~~ +computeCountsGL.h:105:27: warning: 'sequenceContainer computeCountsGL::_sc' [-Wreorder] + 105 | sequenceContainer _sc; + | ^~~ +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): + | ^~~~~~~~~~~~~~~ +computeCountsGL.h:117:17: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] + 117 | MDOUBLE _distanceFromNearestOTUForRecent; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +computeCountsGL.h:113:14: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] + 113 | bool _isSilent; + | ^~~~~~~~~ +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): + | ^~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -1612,7 +1699,8 @@ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, - from gainLossModel.cpp:17: + 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); | ^~~~~~~~ @@ -1635,34 +1723,68 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModel::gainLossModel(double, Vdouble, bool, bool, bool, bool)': -gainLossModel.h:108:17: warning: 'gainLossModel::_gain' will be initialized after [-Wreorder] - 108 | MDOUBLE _gain; // _Q[0][1] - | ^~~~~ -gainLossModel.h:105:17: warning: 'Vdouble gainLossModel::_freq' [-Wreorder] - 105 | Vdouble _freq; +In file included from gainLoss.h:30, + from gainLoss.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.cpp:24:1: warning: when initialized here [-Wreorder] - 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): - | ^~~~~~~~~~~~~ -gainLossModel.h:112:14: warning: 'gainLossModel::_isRootFreqEQstationary' will be initialized after [-Wreorder] - 112 | bool _isRootFreqEQstationary; - | ^~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h:111:14: warning: 'bool gainLossModel::_isReversible' [-Wreorder] - 111 | bool _isReversible; - | ^~~~~~~~~~~~~ -gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] - 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): - | ^~~~~~~~~~~~~ -gainLossModel.h:114:14: warning: 'gainLossModel::_isHGT_with_Q' will be initialized after [-Wreorder] - 114 | bool _isHGT_with_Q; - | ^~~~~~~~~~~~~ -gainLossModel.h:110:15: warning: 'q2pt* gainLossModel::_q2pt' [-Wreorder] - 110 | q2pt *_q2pt; // dont use q2p - | ^~~~~ -gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] - 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): - | ^~~~~~~~~~~~~ +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.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, + | ^~~~~~~~~~~~~~~~~~~~~~~ +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 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 { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +optimizeGainLossModelVV.cpp:76:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] + 76 | MDOUBLE sumPijQij; + | ^~~~~~~~~ +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 { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../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); @@ -1698,7 +1820,6 @@ bblLS.h:152:18: warning: when initialized here [-Wreorder] 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 gainLoss.h: In constructor 'gainLoss::gainLoss()': gainLoss.h:266:28: warning: 'gainLoss::_unObservableData_p' will be initialized after [-Wreorder] 266 | unObservableData* _unObservableData_p; @@ -1727,20 +1848,7 @@ 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) | ^~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)': -gainLoss.cpp:604:14: warning: unused variable 'missigDataChar' [-Wunused-variable] - 604 | char missigDataChar = -2; - | ^~~~~~~~~~~~~~ -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 { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); | ^~~~~~~~ @@ -1757,17 +1865,25 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': -gainLoss.cpp:1245:64: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] - 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ - | ^~ -gainLoss.cpp:1245:45: note: add parentheses around left hand side expression to silence this warning - 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ - | ^~~~~~~~~~~~~~~~~~~ - | ( ) +../../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 { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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) + | ^ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, - from siteSpecificGL.cpp:23: + from gainLossModel.h:27, + from gainLossModel.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ @@ -1775,8 +1891,8 @@ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:30, - from gainLossOptimizer.h:24, - from gainLossOptimizer.cpp:17: + 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); | ^~~~~~~~ @@ -1786,14 +1902,25 @@ ../../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); - | ^~~~~~~~~ -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); - | ^~~~~~~~~ +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): + | ^~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -1810,7 +1937,42 @@ 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 siteSpecificGL.cpp:24: +gainLoss.cpp: In member function 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)': +gainLoss.cpp:604:14: warning: unused variable 'missigDataChar' [-Wunused-variable] + 604 | char missigDataChar = -2; + | ^~~~~~~~~~~~~~ +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; + | ^~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModel::gainLossModel(double, Vdouble, bool, bool, bool, bool)': +gainLossModel.h:108:17: warning: 'gainLossModel::_gain' will be initialized after [-Wreorder] + 108 | MDOUBLE _gain; // _Q[0][1] + | ^~~~~ +gainLossModel.h:105:17: warning: 'Vdouble gainLossModel::_freq' [-Wreorder] + 105 | Vdouble _freq; + | ^~~~~ +gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] + 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): + | ^~~~~~~~~~~~~ +gainLossModel.h:112:14: warning: 'gainLossModel::_isRootFreqEQstationary' will be initialized after [-Wreorder] + 112 | bool _isRootFreqEQstationary; + | ^~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h:111:14: warning: 'bool gainLossModel::_isReversible' [-Wreorder] + 111 | bool _isReversible; + | ^~~~~~~~~~~~~ +gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] + 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): + | ^~~~~~~~~~~~~ +gainLossModel.h:114:14: warning: 'gainLossModel::_isHGT_with_Q' will be initialized after [-Wreorder] + 114 | bool _isHGT_with_Q; + | ^~~~~~~~~~~~~ +gainLossModel.h:110:15: warning: 'q2pt* gainLossModel::_q2pt' [-Wreorder] + 110 | q2pt *_q2pt; // dont use q2p + | ^~~~~ +gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] + 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): + | ^~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -1827,93 +1989,13 @@ 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 gainLossOptimizer.cpp:20: -bblLS.h: At global scope: -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; - | ^~~~~~~~~~~~~~~~~~~ -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 -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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, stochasticProcess*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)': -gainLossOptimizer.h:134:14: warning: 'gainLossOptimizer::_tr' will be initialized after [-Wreorder] - 134 | tree _tr; - | ^~~ -gainLossOptimizer.h:109:28: warning: 'stochasticProcess* gainLossOptimizer::_sp' [-Wreorder] - 109 | stochasticProcess *_sp; - | ^~~ -gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] - 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, - | ^~~~~~~~~~~~~~~~~ -gainLossOptimizer.h:135:27: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] - 135 | sequenceContainer _sc; - | ^~~ -gainLossOptimizer.h:93:17: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] - 93 | MDOUBLE _epsilonOptimization; - | ^~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] - 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, - | ^~~~~~~~~~~~~~~~~ -gainLossOptimizer.h:104:18: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] - 104 | Vdouble* _weightsUniqPatterns; - | ^~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.h:102:28: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] - 102 | unObservableData* _unObservableData_p; - | ^~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] - 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, - | ^~~~~~~~~~~~~~~~~ -gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, std::vector >&, distribution*, distribution*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)': -gainLossOptimizer.h:139:23: warning: 'gainLossOptimizer::_lossDist' will be initialized after [-Wreorder] - 139 | distribution* _lossDist; - | ^~~~~~~~~ -gainLossOptimizer.h:135:27: warning: 'sequenceContainer gainLossOptimizer::_sc' [-Wreorder] - 135 | sequenceContainer _sc; - | ^~~ -gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] - 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, - | ^~~~~~~~~~~~~~~~~ -gainLossOptimizer.h:135:27: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] - 135 | sequenceContainer _sc; - | ^~~ -gainLossOptimizer.h:93:17: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] - 93 | MDOUBLE _epsilonOptimization; - | ^~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] - 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, - | ^~~~~~~~~~~~~~~~~ -gainLossOptimizer.h:104:18: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] - 104 | Vdouble* _weightsUniqPatterns; - | ^~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.h:102:28: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] - 102 | unObservableData* _unObservableData_p; - | ^~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] - 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, - | ^~~~~~~~~~~~~~~~~ +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 gainLoss.h:30, - from gainLossProject.cpp:17: + 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); | ^~~~~~~~ @@ -1939,49 +2021,17 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengths(int)': -gainLossOptimizer.cpp:498:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] - 498 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:543:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] - 543 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:487:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] - 487 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengthsvv(int)': -gainLossOptimizer.cpp:634:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] - 634 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:677:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] - 677 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossOptimizer.cpp:623:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] - 623 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLoss.cpp: In member function 'double gainLoss::computeDistanceFromRootForRecent(tree&)': -gainLoss.cpp:4205:14: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] - 4205 | bool isRecentBiggerAncient = true; - | ^~~~~~~~~~~~~~~~~~~~~ -gainLoss.cpp: In member function 'double gainLoss::computeDistanceNearestOTUforRecent(tree&)': -gainLoss.cpp:4283:14: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] - 4283 | bool isRecentBiggerAncient = true; - | ^~~~~~~~~~~~~~~~~~~~~ -gainLoss.cpp: In member function 'void gainLoss::multipleAllBranchesByFactorAtStart(double)': -gainLoss.cpp:4382:40: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] - 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ - | ^ -gainLoss.cpp:4382:28: note: add parentheses around left hand side expression to silence this warning - 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ - | ^~~~~~~~~~~ - | ( ) -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; - | ^~~~~~ +gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': +gainLoss.cpp:1245:64: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] + 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ + | ^~ +gainLoss.cpp:1245:45: note: add parentheses around left hand side expression to silence this warning + 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ + | ^~~~~~~~~~~~~~~~~~~ + | ( ) In file included from gainLoss.h:30, - from computeCountsGL.h:24, - from computeCountsGL.cpp:17: + 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); | ^~~~~~~~ @@ -1991,32 +2041,13 @@ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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: +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); | ^~~~~~~~ -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 { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2036,89 +2067,6 @@ 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -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; - | ^~~~~~~~~ -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; - | ^~~ -computeCountsGL.h:102:28: warning: 'stochasticProcess* computeCountsGL::_sp' [-Wreorder] - 102 | stochasticProcess *_sp; - | ^~~ -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): - | ^~~~~~~~~~~~~~~ -computeCountsGL.h:117:17: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] - 117 | MDOUBLE _distanceFromNearestOTUForRecent; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -computeCountsGL.h:113:14: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] - 113 | bool _isSilent; - | ^~~~~~~~~ -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): - | ^~~~~~~~~~~~~~~ -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; - | ^~~~~~~~~ -computeCountsGL.h:105:27: warning: 'sequenceContainer computeCountsGL::_sc' [-Wreorder] - 105 | sequenceContainer _sc; - | ^~~ -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): - | ^~~~~~~~~~~~~~~ -computeCountsGL.h:117:17: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] - 117 | MDOUBLE _distanceFromNearestOTUForRecent; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -computeCountsGL.h:113:14: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] - 113 | bool _isSilent; - | ^~~~~~~~~ -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): - | ^~~~~~~~~~~~~~~ -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): - | ^~~~~~~~~~~ -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; - | ^~~~~~~~~~~~ -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 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 -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 { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -2135,111 +2083,8 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/iostream:41, - from ../../libs/phylogeny/readTree.h:6, - from ../../libs/phylogeny/tree.h:7, - from ../../libs/phylogeny/simulateJumpsAbstract.h:5, - from ../../libs/phylogeny/simulateJumps.h:4, - from computePosteriorExpectationOfChange.h:24, - from computePosteriorExpectationOfChange.cpp:17: -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3: -/usr/include/c++/14/ostream:232:25: warning: 'Down' may be used uninitialized [-Wmaybe-uninitialized] - 232 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': -computePosteriorExpectationOfChange.cpp:215:27: note: 'Down' was declared here - 215 | doubleRep resDXY, Down, Up; - | ^~~~ -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3: -/usr/include/c++/14/ostream:232:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] - 232 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': -computePosteriorExpectationOfChange.cpp:215:33: note: 'Up' was declared here - 215 | doubleRep resDXY, Down, Up; - | ^~ -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3: -/usr/include/c++/14/ostream:232:25: warning: 'pij' may be used uninitialized [-Wmaybe-uninitialized] - 232 | { return _M_insert(__f); } - | ~~~~~~~~~^~~~~ -computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': -computePosteriorExpectationOfChange.cpp:216:17: note: 'pij' was declared here - 216 | MDOUBLE pij; - | ^~~ -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 -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; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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) - | ^~~~ -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){ - | ^~~~~~~~~~~~~ - | ( ) -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 gainLoss.h:30, - from gainLoss4site.h:24, - from gainLoss4site.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); | ^~~~~~~~ @@ -2249,22 +2094,10 @@ ../../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) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~ 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; @@ -2284,60 +2117,54 @@ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, | ^~~~~~~~~~~~~ -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 { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~ +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): + | ^~~~~~~~~~~ +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; + | ^~~~~~~~~~~~ In file included from gainLoss.h:30, - from simulateChangesAlongTree.cpp:20: + 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); | ^~~~~~~~ -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); - | ^~~~ 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 { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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; - | ^~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ @@ -2354,26 +2181,9 @@ 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) - | ^~~~ -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 { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:30, - from simulateOnePos.cpp:32: + 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); | ^~~~~~~~ @@ -2428,25 +2238,6 @@ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile | ^~~~~~~~~~~~~~ -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): - | ^~~~~~~~~~~~~~~~~~~~ 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; @@ -2454,15 +2245,265 @@ simulateOnePos.cpp:202:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] 202 | MDOUBLE sumQii = 1.0; | ^~~~~~ -ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o -ar: creating libindelCoder.a -a - indelCoder.o -a - indelCoderOptions.o -a - indelCoderProject.o -a - indelCoderUtils.o -a - character.o -a - gaps.o -ranlib libindelCoder.a +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 + | ^~~~~~~~~~~~~ +gainLoss.cpp: In member function 'double gainLoss::computeDistanceFromRootForRecent(tree&)': +gainLoss.cpp:4205:14: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] + 4205 | bool isRecentBiggerAncient = true; + | ^~~~~~~~~~~~~~~~~~~~~ +gainLoss.cpp: In member function 'double gainLoss::computeDistanceNearestOTUforRecent(tree&)': +gainLoss.cpp:4283:14: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] + 4283 | bool isRecentBiggerAncient = true; + | ^~~~~~~~~~~~~~~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::multipleAllBranchesByFactorAtStart(double)': +gainLoss.cpp:4382:40: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] + 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ + | ^ +gainLoss.cpp:4382:28: note: add parentheses around left hand side expression to silence this warning + 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ + | ^~~~~~~~~~~ + | ( ) +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; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + 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, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, stochasticProcess*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)': +gainLossOptimizer.h:134:14: warning: 'gainLossOptimizer::_tr' will be initialized after [-Wreorder] + 134 | tree _tr; + | ^~~ +gainLossOptimizer.h:109:28: warning: 'stochasticProcess* gainLossOptimizer::_sp' [-Wreorder] + 109 | stochasticProcess *_sp; + | ^~~ +gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] + 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, + | ^~~~~~~~~~~~~~~~~ +gainLossOptimizer.h:135:27: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] + 135 | sequenceContainer _sc; + | ^~~ +gainLossOptimizer.h:93:17: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] + 93 | MDOUBLE _epsilonOptimization; + | ^~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] + 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, + | ^~~~~~~~~~~~~~~~~ +gainLossOptimizer.h:104:18: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] + 104 | Vdouble* _weightsUniqPatterns; + | ^~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.h:102:28: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] + 102 | unObservableData* _unObservableData_p; + | ^~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] + 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, + | ^~~~~~~~~~~~~~~~~ +gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, std::vector >&, distribution*, distribution*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)': +gainLossOptimizer.h:139:23: warning: 'gainLossOptimizer::_lossDist' will be initialized after [-Wreorder] + 139 | distribution* _lossDist; + | ^~~~~~~~~ +gainLossOptimizer.h:135:27: warning: 'sequenceContainer gainLossOptimizer::_sc' [-Wreorder] + 135 | sequenceContainer _sc; + | ^~~ +gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] + 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, + | ^~~~~~~~~~~~~~~~~ +gainLossOptimizer.h:135:27: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] + 135 | sequenceContainer _sc; + | ^~~ +gainLossOptimizer.h:93:17: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] + 93 | MDOUBLE _epsilonOptimization; + | ^~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] + 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, + | ^~~~~~~~~~~~~~~~~ +gainLossOptimizer.h:104:18: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] + 104 | Vdouble* _weightsUniqPatterns; + | ^~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.h:102:28: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] + 102 | unObservableData* _unObservableData_p; + | ^~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] + 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, + | ^~~~~~~~~~~~~~~~~ +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 '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; + | ^~~~~~ +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){ + | ^~~~~~~~~~~~~ + | ( ) +gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengths(int)': +gainLossOptimizer.cpp:498:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] + 498 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp:543:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] + 543 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp:487:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] + 487 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengthsvv(int)': +gainLossOptimizer.cpp:634:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] + 634 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossOptimizer.cpp:677:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] + 677 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + | ^~~~~~~~~~~~~ +gainLossOptimizer.cpp:623:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] + 623 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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, + from ../../libs/phylogeny/simulateJumpsAbstract.h:5, + from ../../libs/phylogeny/simulateJumps.h:4, + from computePosteriorExpectationOfChange.h:24, + from computePosteriorExpectationOfChange.cpp:17: +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3: +/usr/include/c++/14/ostream:232:25: warning: 'Down' may be used uninitialized [-Wmaybe-uninitialized] + 232 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': +computePosteriorExpectationOfChange.cpp:215:27: note: 'Down' was declared here + 215 | doubleRep resDXY, Down, Up; + | ^~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3: +/usr/include/c++/14/ostream:232:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] + 232 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': +computePosteriorExpectationOfChange.cpp:215:33: note: 'Up' was declared here + 215 | doubleRep resDXY, Down, Up; + | ^~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3: +/usr/include/c++/14/ostream:232:25: warning: 'pij' may be used uninitialized [-Wmaybe-uninitialized] + 232 | { return _M_insert(__f); } + | ~~~~~~~~~^~~~~ +computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': +computePosteriorExpectationOfChange.cpp:216:17: note: 'pij' was declared here + 216 | MDOUBLE pij; + | ^~~ +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; + | ^~~ +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; + | ^~~~~~~~~~ +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; + | ^~~~~~~~~ +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; + | ^~ +gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const std::string&)': +gainLossOptions.cpp:2064:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] + 2064 | return returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp:2047:27: note: 'returnType' was declared here + 2047 | optimizationLevel returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const std::string&)': +gainLossOptions.cpp:2419:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] + 2419 | return returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp:2396:24: note: 'returnType' was declared here + 2396 | simulationType returnType; + | ^~~~~~~~~~ ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o ar: creating libfastml.a a - fastml.o @@ -2479,22 +2520,8 @@ a - mainbb.o a - sequenceDataDiff.o a - suffStatComponentJointNoGamma.o -g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder ranlib libfastml.a -gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const std::string&)': -gainLossOptions.cpp:2064:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] - 2064 | return returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp:2047:27: note: 'returnType' was declared here - 2047 | optimizationLevel returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const std::string&)': -gainLossOptions.cpp:2419:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] - 2419 | return returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp:2396:24: note: 'returnType' was declared here - 2396 | simulationType returnType; - | ^~~~~~~~~~ +g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': gainLossOptimizer.cpp:833:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] 833 | return res; @@ -2502,8 +2529,17 @@ gainLossOptimizer.cpp:820:43: note: 'res' was declared here 820 | gainLossOptions::distributionType res; | ^~~ +ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o +ar: creating libindelCoder.a +a - indelCoder.o +a - indelCoderOptions.o +a - indelCoderProject.o +a - indelCoderUtils.o +a - character.o +a - gaps.o +ranlib libindelCoder.a +g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' -g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' In member function 'void gainLossModelNonReversible::updateQ()', inlined from 'void gainLossModelNonReversible::setMu2(double)' at gainLossModel.h:156:10, @@ -2656,7 +2692,7 @@ make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' make[1]: Leaving directory '/build/reproducible-path/fastml-3.11' dh_auto_test - make -j20 test + make -j42 test make[1]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make test cd programs;make test @@ -2667,13 +2703,13 @@ cd gainLoss && make test cd indelCoder && make test make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' if [ -d tests ] ; then cd tests && make -k ; fi +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' if [ -d tests ] ; then cd tests && make -k ; fi make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' -make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' if [ -d tests ] ; then cd tests && make -k ; fi +make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' @@ -2688,24 +2724,24 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistanceK2P.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistanceK2P g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. doubleRep.cpp ../libEvolTree.a -lEvolTree -o doubleRep g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. readTreeWithComments.cpp ../libEvolTree.a -lEvolTree -o readTreeWithComments -./doubleRep > doubleRep.out.tmp -diff doubleRep.out.tmp doubleRep.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 +./doubleRep > doubleRep.out.tmp +diff doubleRep.out.tmp doubleRep.out.standard ./splitMap_test > splitMap_test.out.tmp diff splitMap_test.out.tmp splitMap_test.out.standard -./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp -diff readTreeWithComments.out.tmp readTreeWithComments.out.standard ./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp -./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp -./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp +./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard -diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard -diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard +diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard ./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard -./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp -diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard +./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp +./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp +diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard +diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.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 -j20 install DESTDIR=/build/reproducible-path/fastml-3.11/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j42 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' @@ -2729,14 +2765,14 @@ cd fastml && make install cd gainLoss && make install cd indelCoder && make install -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' -mkdir -p ../../bin 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/gainLoss' +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' mkdir -p ../../bin cp indelCoder ../../bin/indelCoder cp fastml ../../bin/fastml +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' +mkdir -p ../../bin cp gainLoss ../../bin/gainLoss make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' @@ -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/1690579/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1690579/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/3550313 and its subdirectories -I: Current time: Sun Mar 2 00:46:34 -12 2025 -I: pbuilder-time-stamp: 1740919594 +I: removing directory /srv/workspace/pbuilder/1690579 and its subdirectories +I: Current time: Sun Apr 5 09:11:34 +14 2026 +I: pbuilder-time-stamp: 1775329894