Diff of the two buildlogs: -- --- b1/build.log 2025-01-20 09:51:05.540030779 +0000 +++ b2/build.log 2025-01-20 09:58:48.331105489 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 19 21:35:43 -12 2025 -I: pbuilder-time-stamp: 1737365743 +I: Current time: Mon Jan 20 23:51:53 +14 2025 +I: pbuilder-time-stamp: 1737366713 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/9244/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/21011/tmp/hooks/D01_modify_environment starting +debug: Running on virt64z. +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 Jan 20 09:52 /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/21011/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/21011/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='72275b3e191747c49edfaefea3dab3fa' - 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='9244' - PS1='# ' - PS2='> ' + INVOCATION_ID=5929b74f6a0740f7b04f6bbed372b747 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=21011 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.lnMaC55b/pbuilderrc_NQYu --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lnMaC55b/b1 --logfile b1/build.log fastml_3.11-4.dsc' - SUDO_GID='112' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.lnMaC55b/pbuilderrc_WMcI --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lnMaC55b/b2 --logfile b2/build.log fastml_3.11-4.dsc' + SUDO_GID=110 + SUDO_UID=103 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32b 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/9244/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/21011/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -142,7 +174,7 @@ Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.23 [919 kB] -Fetched 19.6 MB in 1s (28.3 MB/s) +Fetched 19.6 MB in 3s (7255 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19569 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/21011/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/21011/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 @@ -289,28 +325,28 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/fastml-3.11' dh_auto_clean - make -j3 clean + make -j4 clean make[2]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make clean cd programs;make clean make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs' -cd phylogeny && make clean make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs' cd fastml && make clean +cd phylogeny && make clean cd gainLoss && make clean -make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' 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 -rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o -make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' -cd indelCoder && make clean make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' +cd indelCoder && make clean make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' -make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/libs' +make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' +rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o +make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o +make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' make[2]: Leaving directory '/build/reproducible-path/fastml-3.11' @@ -328,7 +364,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "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' @@ -345,11 +381,13 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o alphabet.o alphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o amino.o amino.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlpha.o bestAlpha.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)': bestAlpha.cpp:371:17: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] 371 | MDOUBLE oldA=0; | ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.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 @@ -360,8 +398,6 @@ bestAlphaManyTrees.cpp:184:23: warning: variable 'cx' set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from bestAlpha.h:6, @@ -376,6 +412,8 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from bestHKYparam.h:6, @@ -384,18 +422,19 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bestHkyParamAlphaAndBBLProportional::bestHkyParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)' at bestHKYparam.cpp:197:18: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from bblEM.h:5, @@ -404,17 +443,14 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeCounts.o computeCounts.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void bblEMProportionalEB::allocatePlacePropEB()' at bblEMProportionalEB.cpp:106:31: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeMarginalAlg.o computeMarginalAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp @@ -428,6 +464,7 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void codonUtility::readCodonUsage(const std::string&, Vdouble&, const codon&)' at codon.cpp:460:19: @@ -444,21 +481,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp -In file included from /usr/include/c++/14/vector:72, - from definitions.h:18, - from computeUpAlgFactors.cpp:3: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeUpAlg::fillComputeUpSpecificGlobalRateFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double, std::vector&)' at computeUpAlgFactors.cpp:128:16: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] @@ -479,6 +501,21 @@ 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): | ^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from definitions.h:18, + from computeUpAlgFactors.cpp:3: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void computeUpAlg::fillComputeUpSpecificGlobalRateFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double, std::vector&)' at computeUpAlgFactors.cpp:128:16: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&, std::vector&)' at computeUpAlgFactors.cpp:42:16: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -489,7 +526,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp In file included from /usr/include/c++/14/iostream:41, from readTree.h:6, @@ -553,6 +589,8 @@ 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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from computeSubstitutionCounts.h:4: @@ -560,7 +598,8 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeSubstitutionCounts::run()' at computeSubstitutionCounts.cpp:38:62: @@ -572,7 +611,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:356:43: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -583,13 +622,8 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:225:48: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from distanceTable.cpp:3: @@ -603,12 +637,15 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:225:48: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from fastStartTree.cpp:15: @@ -649,7 +686,6 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp @@ -666,6 +702,7 @@ 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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from generalGammaDistributionFixedCategories.h:9, @@ -680,13 +717,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from definitions.h:18, - from fromQtoPt.cpp:3: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void generalGammaDistributionFixedCategories::fill_mean()' at generalGammaDistributionFixedCategories.cpp:72:15: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -704,17 +734,32 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from definitions.h:18, + from fromQtoPt.cpp:3: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'VVdouble get1PamFromCountMatrix(const std::vector&, const VVdouble&)' at fromQtoPt.cpp:256:17: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.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): + | ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from generalGammaDistribution.h:11, @@ -743,6 +788,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void generalGammaDistribution::setGammaParameters(int, double, double)' at generalGammaDistribution.cpp:70:19, inlined from 'virtual void generalGammaDistribution::change_number_of_categories(int)' at generalGammaDistribution.cpp:52:20: @@ -763,16 +809,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from goldmanYangModel.h:6, @@ -798,8 +835,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp In file included from generalGammaDistributionPlusInvariant.h:9, from simulateWithDependence.h:35, from simulateWithDependence.cpp:1: @@ -809,7 +844,9 @@ generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.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, @@ -827,13 +864,13 @@ 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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.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); @@ -841,7 +878,6 @@ 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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, @@ -850,6 +886,7 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:141:38: @@ -871,7 +908,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp 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*&)': @@ -879,6 +915,14 @@ 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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp +numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] + 306 | //* for (i=1;i >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp -numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] - 306 | //* for (i=1;i >' changed in GCC 7.1 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from 'double performKSTest(const uniformDistribution&, Vdouble&)' at numRec.cpp:465:6: @@ -967,12 +1005,11 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from readDatMatrix.h:6, @@ -997,7 +1034,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequence.o sequence.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:95:52: @@ -1009,6 +1045,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequenceContainer.o sequenceContainer.cpp sequence.cpp: In constructor 'sequence::sequence(const sequence&, const alphabet*)': sequence.cpp:76:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 76 | || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) @@ -1025,8 +1062,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequenceContainer.o sequenceContainer.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.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; @@ -1035,7 +1070,6 @@ sequenceContainer.cpp:199:14: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] 199 | bool gapCol; | ^~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o siteSpecificRate.o siteSpecificRate.cpp sequenceContainer.cpp: In member function 'int sequenceContainer::getNumOfOccurancesPerPos(int, char)': sequenceContainer.cpp:452:19: warning: unused variable 'len' [-Wunused-variable] 452 | const int len = _seqDataVec[0].seqLen(); @@ -1044,10 +1078,10 @@ sequenceContainer.cpp:467:19: warning: unused variable 'len' [-Wunused-variable] 467 | const int len = _seqDataVec[0].seqLen(); | ^~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o split.o split.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from someUtil.cpp:9: @@ -1104,18 +1138,11 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp -tree.cpp: In constructor 'tree::tree(const std::string&)': -tree.cpp:180:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 180 | if (in.is_open()) - | ^~ -tree.cpp:182:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 182 | create_names_to_internal_nodes(); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1589:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1589 | __heap_select(_RandomAccessIterator __first, @@ -1162,6 +1189,7 @@ /usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1908 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from 'double computeQuantileFrac(const std::vector&, double)' at someUtil.cpp:113:6: @@ -1291,7 +1319,15 @@ /usr/include/c++/14/bits/stl_algo.h:1908:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1908 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp +tree.cpp: In constructor 'tree::tree(const std::string&)': +tree.cpp:180:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 180 | if (in.is_open()) + | ^~ +tree.cpp:182:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 182 | create_names_to_internal_nodes(); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.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] @@ -1301,6 +1337,7 @@ 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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from uniformDistribution.h:22, @@ -1328,12 +1365,10 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from GLaguer.cpp:2: @@ -1362,6 +1397,7 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.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*)': @@ -1392,6 +1428,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from replacementModel.h:6, @@ -1407,10 +1444,12 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp In file included from betaDistribution.cpp:3: betaDistribution.h: In copy constructor 'betaDistribution::betaDistribution(const betaDistribution&)': betaDistribution.h:54:25: warning: 'betaDistribution::_boundary' will be initialized after [-Wreorder] @@ -1422,6 +1461,7 @@ betaDistribution.cpp:23:1: warning: when initialized here [-Wreorder] 23 | betaDistribution::betaDistribution(const betaDistribution& other) : | ^~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from betaDistribution.h:10: @@ -1429,7 +1469,6 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void betaDistribution::setBetaParameters(int, double, double)' at betaDistribution.cpp:86:19: @@ -1470,9 +1509,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp @@ -1484,6 +1520,10 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o extremeValDistribution.o extremeValDistribution.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from bestTamura92param.h:6, @@ -1492,16 +1532,6 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double, double)' at bestTamura92param.cpp:250:18: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o extremeValDistribution.o extremeValDistribution.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp In file included from generalGammaDistributionPlusInvariant.h:9, @@ -1512,8 +1542,12 @@ 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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double, double)' at bestTamura92param.cpp:250:18: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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=] @@ -1522,7 +1556,11 @@ 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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.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] @@ -1534,12 +1572,11 @@ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] 256 | computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) | ^~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp In file included from seqeuncesFilter.h:6, from seqeuncesFilter.cpp:1: In member function 'const sequence& sequenceContainer::operator[](int) const', @@ -1551,6 +1588,7 @@ 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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from simulateJumpsAbstract.h:4, @@ -1560,14 +1598,12 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void simulateJumps::init()' at simulateJumps.cpp:63:23: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.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; @@ -1650,6 +1686,7 @@ mixtureDistribution.cpp:40:43: note: 'pComp' declared here 40 | generalGammaDistribution* pComp; | ^~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp In member function 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]', inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]' at /usr/include/c++/14/bits/alloc_traits.h:569:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1288:30, @@ -1673,8 +1710,8 @@ 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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from suffStatGammaMixture.h:16, @@ -1708,7 +1745,6 @@ 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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp In file included from optGammaMixtureEM.cpp:1: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': optGammaMixtureEM.h:76:25: warning: unused variable 'res1' [-Wunused-variable] @@ -1718,26 +1754,7 @@ optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable] 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algo.h:61, - from /usr/include/c++/14/algorithm:61, - from optGammaMixtureEM.cpp:7: -/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1770 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1876 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from GamMixtureOptimizer.cpp:7: @@ -1758,6 +1775,7 @@ /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from 'double GamMixtureOptimizer::findBestParamManyStarts(Vint, Vint, std::vector, Vdouble, const Vdouble*, std::ofstream*)' at GamMixtureOptimizer.cpp:73:8: @@ -1809,8 +1827,27 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1907 | __comp); | ~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp +In file included from /usr/include/c++/14/bits/stl_algo.h:61, + from /usr/include/c++/14/algorithm:61, + from optGammaMixtureEM.cpp:7: +/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1770 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1876 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from 'double optGammaMixtureEM::findBestParamManyStarts(int, int, int, int, double, double, std::ofstream*)' at optGammaMixtureEM.cpp:64:6: @@ -1831,27 +1868,7 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp -In file included from /usr/include/c++/14/vector:72, - from definitions.h:18, - from replacementModel.h:6, - from wYangModel.h:4, - from wYangModel.cpp:1: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'wYangModel::wYangModel(double, double, bool, codon*)' at wYangModel.cpp:11:47: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'wYangModel::wYangModel(double, double, const Vdouble&, bool, codon*)' at wYangModel.cpp:20:47: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from codonUtils.cpp:3: @@ -1881,12 +1898,32 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from definitions.h:18, + from replacementModel.h:6, + from wYangModel.h:4, + from wYangModel.cpp:1: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'Vdouble freqCodonF3x4(const sequenceContainer&, codon*)' at codonUtils.cpp:73:25: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'wYangModel::wYangModel(double, double, bool, codon*)' at wYangModel.cpp:11:47: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'wYangModel::wYangModel(double, double, const Vdouble&, bool, codon*)' at wYangModel.cpp:20:47: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from 'void kaks2Color(const Vdouble&, const Vdouble&, const sequence&, std::string, codon*)' at codonUtils.cpp:246:7: @@ -1907,13 +1944,13 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp In file included from /usr/include/c++/14/vector:72, from definitions.h:18, from betaDistributionFixedCategories.h:9, @@ -1951,12 +1988,10 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestGtrModelParams.o bestGtrModelParams.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] @@ -1968,6 +2003,7 @@ gtrModel.cpp:5:1: warning: when initialized here [-Wreorder] 5 | gtrModel::gtrModel(const Vdouble& freq, | ^~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp gtrModel.cpp: In member function 'double gtrModel::get_a2c() const': gtrModel.cpp:139:16: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] @@ -1976,6 +2012,17 @@ gtrModel.cpp:130:17: note: 'result' was declared here 130 | MDOUBLE result; | ^~~~~~ +In file included from bestGtrModelParams.cpp:3: +bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': +bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] + 175 | stochasticProcess& _sp; + | ^~~ +bestGtrModelParams.h:173:34: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] + 173 | const gammaDistribution* _pProportionDist; + | ^~~~~~~~~~~~~~~~ +bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] + 162 | C_evalGTRParamProportional( const GTRParam param, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_a2g() const': gtrModel.cpp:153:16: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 153 | return result; @@ -1997,17 +2044,6 @@ gtrModel.cpp:172:17: note: 'result' was declared here 172 | MDOUBLE result; | ^~~~~~ -In file included from bestGtrModelParams.cpp:3: -bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': -bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] - 175 | stochasticProcess& _sp; - | ^~~ -bestGtrModelParams.h:173:34: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] - 173 | const gammaDistribution* _pProportionDist; - | ^~~~~~~~~~~~~~~~ -bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] - 162 | C_evalGTRParamProportional( const GTRParam param, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_c2t() const': gtrModel.cpp:195:16: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 195 | return result; @@ -2226,14 +2262,15 @@ make[2]: Entering directory '/build/reproducible-path/fastml-3.11/programs' cd fastml && make all cd gainLoss && make all -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' cd indelCoder && make all +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' making depend -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' 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 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': indelCoder.cpp:422:13: warning: unused variable 'gapNum' [-Wunused-variable] 422 | int gapNum = 1; @@ -2246,6 +2283,7 @@ 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 -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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp In file included from bbAlg.h:8, from fastml.cpp:254: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': @@ -2264,8 +2302,9 @@ 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 -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 -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 -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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp In file included from bbAlg.h:8, from bbAlg.cpp:1: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': @@ -2310,6 +2349,14 @@ indelCoder.cpp:170:22: note: 'condition' was declared here 170 | bool condition; | ^~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o character.o character.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; + | ^~~~~~~~~~~~~~~~~ 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; @@ -2317,49 +2364,28 @@ gainLossOptions.cpp:2098:24: note: 'returnType' was declared here 2098 | costMatrixType returnType; | ^~~~~~~~~~ +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]){ + | ^ +character.cpp:17:13: note: 'longestGapStIndex' was declared here + 17 | int longestGapStIndex; + | ^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp -gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const std::string&)': -gainLossOptions.cpp:2064:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] - 2064 | return returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp:2047:27: note: 'returnType' was declared here - 2047 | optimizationLevel returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const std::string&)': -gainLossOptions.cpp:2419:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] - 2419 | return returnType; - | ^~~~~~~~~~ -gainLossOptions.cpp:2396:24: note: 'returnType' was declared here - 2396 | simulationType returnType; - | ^~~~~~~~~~ +ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o +ar: creating libindelCoder.a +a - indelCoder.o +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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp -In file included from bbEvaluateSpecificAV.cpp:1: -bbEvaluateSpecificAV.h: In constructor 'bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&)': -bbEvaluateSpecificAV.h:34:34: warning: 'bbEvaluateSpecificAV::_sc' will be initialized after [-Wreorder] - 34 | const sequenceContainer& _sc; - | ^~~ -bbEvaluateSpecificAV.h:31:30: warning: 'const computePijGam& bbEvaluateSpecificAV::_bbcpij' [-Wreorder] - 31 | const computePijGam& _bbcpij; - | ^~~~~~~ -bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] - 3 | bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, - | ^~~~~~~~~~~~~~~~~~~~ -bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': -bbEvaluateSpecificAV.cpp:65:33: warning: unused variable 'rate' [-Wunused-variable] - 65 | MDOUBLE rate = _sp.rates(categor); // the r. - | ^~~~ -In file included from bbEvaluateSpecificAV.h:4: -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp 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=] @@ -2466,29 +2492,25 @@ gainLoss.cpp:1868:25: warning: unused variable 'sumPijQij' [-Wunused-variable] 1868 | MDOUBLE sumPijQij = normalizeQ(sp); | ^~~~~~~~~ -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; - | ^~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~ -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]){ - | ^ -character.cpp:17:13: note: 'longestGapStIndex' was declared here - 17 | int longestGapStIndex; - | ^~~~~~~~~~~~~~~~~ -In file included from bbfindBestAVDynProg.h:5, - from bbfindBestAVDynProg.cpp:1: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp +gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const std::string&)': +gainLossOptions.cpp:2064:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] + 2064 | return returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp:2047:27: note: 'returnType' was declared here + 2047 | optimizationLevel returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const std::string&)': +gainLossOptions.cpp:2419:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] + 2419 | return returnType; + | ^~~~~~~~~~ +gainLossOptions.cpp:2396:24: note: 'returnType' was declared here + 2396 | simulationType returnType; + | ^~~~~~~~~~ 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; @@ -2509,19 +2531,33 @@ gainLoss.cpp:4951:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] 4951 | MDOUBLE sumQii = 1.0; | ^~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp -ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o -ar: creating libindelCoder.a -a - indelCoder.o -a - indelCoderOptions.o -a - indelCoderProject.o -a - indelCoderUtils.o -a - character.o -a - gaps.o +In file included from bbEvaluateSpecificAV.cpp:1: +bbEvaluateSpecificAV.h: In constructor 'bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&)': +bbEvaluateSpecificAV.h:34:34: warning: 'bbEvaluateSpecificAV::_sc' will be initialized after [-Wreorder] + 34 | const sequenceContainer& _sc; + | ^~~ +bbEvaluateSpecificAV.h:31:30: warning: 'const computePijGam& bbEvaluateSpecificAV::_bbcpij' [-Wreorder] + 31 | const computePijGam& _bbcpij; + | ^~~~~~~ +bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] + 3 | bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, + | ^~~~~~~~~~~~~~~~~~~~ +bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': +bbEvaluateSpecificAV.cpp:65:33: warning: unused variable 'rate' [-Wunused-variable] + 65 | MDOUBLE rate = _sp.rates(categor); // the r. + | ^~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp +In file included from bbEvaluateSpecificAV.h:4: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] + 62 | static const string usege_splash_screen() { + | ^~~~~~~~~~~~~~~~~~~ +In file included from bbfindBestAVDynProg.h:5, + from bbfindBestAVDynProg.cpp:1: +bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] + 62 | static const string usege_splash_screen() { + | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp -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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bb_options.o bb_options.cpp In file included from bbNodeOrderAlg.cpp:1: bbNodeOrderAlg.h: In constructor 'bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)': @@ -2608,16 +2644,16 @@ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ +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 bbNodeOrderAlg.h:5: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from bbNodeOrderAlg.cpp:5: @@ -2651,17 +2687,7 @@ /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 -In file included from bbReport.cpp:1: -bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': -bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] - 14 | const string& _reportFileName; - | ^~~~~~~~~~~~~~~ -bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] - 13 | const int _minNumOfNodesToVisit; - | ^~~~~~~~~~~~~~~~~~~~~ -bbReport.h:10:18: warning: when initialized here [-Wreorder] - 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) - | ^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from 'std::vector bbNodeOrderAlg::findBestOrderInNode(tree::nodeP, int) const' at bbNodeOrderAlg.cpp:126:6: @@ -2682,16 +2708,66 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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; +In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, + from gainLossUtils.h:27, + from gainLossUtils.cpp:17: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from gainLossUtils.cpp:19: +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +../../libs/phylogeny/distributionPlusInvariant.h: At global scope: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +In file included from gainLossUtils.cpp:20: +../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' + 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossUtils.cpp: In function 'void printTreeWithValuesAsBP(std::ostream&, tree::TreeNode* const&, Vstring, VVVdouble*, bool)': +gainLossUtils.cpp:72:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + 72 | if(probs) + | ^ +gainLossUtils.cpp:88:27: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + 88 | if(probs) + | ^ +gainLossUtils.cpp: In function 'void updateGainBeta(double, std::vector >&, distribution*, distribution*, bool)': +gainLossUtils.cpp:481:17: warning: variable 'normFactor' set but not used [-Wunused-but-set-variable] + 481 | MDOUBLE normFactor; + | ^~~~~~~~~~ +gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': +gainLossUtils.cpp:788:17: warning: unused variable 'scale' [-Wunused-variable] + 788 | MDOUBLE scale; + | ^~~~~ +In file included from bbReport.cpp:1: +bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': +bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] + 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ -bbReport.h:51:19: warning: 'const int BandBReport::_position' [-Wreorder] - 51 | const int _position; - | ^~~~~~~~~ -bbReport.cpp:10:1: warning: when initialized here [-Wreorder] - 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : - | ^~~~~~~~~~~ +bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] + 13 | const int _minNumOfNodesToVisit; + | ^~~~~~~~~~~~~~~~~~~~~ +bbReport.h:10:18: warning: when initialized here [-Wreorder] + 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) + | ^~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from 'void bbNodeOrderAlg::rankRemainingNodesAccordingToTheirMarginalProb(int)' at bbNodeOrderAlg.cpp:70:6: @@ -2712,8 +2788,17 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +bbReport.h: In constructor 'BandBReport::BandBReport(const std::string&, int, int)': +bbReport.h:53:23: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder] + 53 | const string& _reportFileName; + | ^~~~~~~~~~~~~~~ +bbReport.h:51:19: warning: 'const int BandBReport::_position' [-Wreorder] + 51 | const int _position; + | ^~~~~~~~~ +bbReport.cpp:10:1: warning: when initialized here [-Wreorder] + 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : + | ^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': computeMarginalReconstruction.cpp:67:25: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] 67 | MDOUBLE likelihoodOfPos = 0; @@ -2721,6 +2806,20 @@ computeMarginalReconstruction.cpp:45:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp +In file included from /usr/include/c++/14/algorithm:61, + from computeMarginalReconstruction.cpp:8: +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': +/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 + 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': jointNoGamma.cpp:23:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] 23 | MDOUBLE totalLikelihoodOfReconstruction = 0; @@ -2729,12 +2828,6 @@ jointNoGamma.cpp:108:33: warning: unused variable 'maxL' [-Wunused-variable] 108 | MDOUBLE maxL = VERYSMALL; | ^~~~ -In file included from /usr/include/c++/14/algorithm:61, - from computeMarginalReconstruction.cpp:8: -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': -/usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 - 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 1770 | __insertion_sort(_RandomAccessIterator __first, @@ -2745,22 +2838,6 @@ /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 - 1876 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 -/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 - 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from ../../libs/phylogeny/definitions.h:18, - from computeMarginalReconstruction.h:4, - from computeMarginalReconstruction.cpp:1: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In member function 'void gainLossModelNonReversible::updateQ()', inlined from 'void gainLossModelNonReversible::setMu2(double)' at gainLossModel.h:156:10, inlined from 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)' at gainLoss.cpp:1857:100: @@ -2771,26 +2848,14 @@ gainLoss.cpp:1842:17: note: 'currM2' was declared here 1842 | MDOUBLE currM2; | ^~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >*, vector > > >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, - inlined from 'void computeMarginalReconstruction::outputTheMarginalProbForEachCharForEachNodePos(std::ostream&, int)' at computeMarginalReconstruction.cpp:177:7: -/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 - 1905 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1906 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1907 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >*, vector > > >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, - inlined from 'void computeMarginalReconstruction::outputTheMarginalProbForEachCharForEachNodePos(std::ostream&, int)' at computeMarginalReconstruction.cpp:177:7: -/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 - 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 - 1822 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 + 1876 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 +/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 + 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': gainLoss.cpp:1974:39: warning: 'currGainBeta' may be used uninitialized [-Wmaybe-uninitialized] 1974 | updateGainBeta(currGainBeta,spVVec,gainDist,lossDist); @@ -2822,37 +2887,42 @@ gainLoss.cpp:1930:17: note: 'bestGainProbInvariant' was declared here 1930 | MDOUBLE bestGainProbInvariant = 0.5; | ^~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from ../../libs/phylogeny/definitions.h:18, + from computeMarginalReconstruction.h:4, + from computeMarginalReconstruction.cpp:1: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >*, vector > > >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, + inlined from 'void computeMarginalReconstruction::outputTheMarginalProbForEachCharForEachNodePos(std::ostream&, int)' at computeMarginalReconstruction.cpp:177:7: +/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 + 1905 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1906 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1907 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >*, vector > > >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, + inlined from 'void computeMarginalReconstruction::outputTheMarginalProbForEachCharForEachNodePos(std::ostream&, int)' at computeMarginalReconstruction.cpp:177:7: +/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 + 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 + 1822 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'computeMarginalReconstruction::computeMarginalReconstruction(const tree&, std::vector&, const sequenceContainer&)' at computeMarginalReconstruction.cpp:24:28: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp -In file included from bbAlg.h:8, - from mainbb.cpp:5: -bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': -bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] - 14 | const string& _reportFileName; - | ^~~~~~~~~~~~~~~ -bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] - 13 | const int _minNumOfNodesToVisit; - | ^~~~~~~~~~~~~~~~~~~~~ -bbReport.h:10:18: warning: when initialized here [-Wreorder] - 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) - | ^~~~~~~~~~~~~~~~~ -In file included from 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] - 175 | stochasticProcess& _sp; - | ^~~ -../../libs/phylogeny/bestGtrModelParams.h:173:34: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] - 173 | const gammaDistribution* _pProportionDist; - | ^~~~~~~~~~~~~~~~ -../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] - 162 | C_evalGTRParamProportional( const GTRParam param, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/iostream:41, from ../../libs/phylogeny/readTree.h:6, from ../../libs/phylogeny/tree.h:7, @@ -2887,132 +2957,6 @@ gainLoss.cpp:3852:37: note: 'Theta' was declared here 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; | ^~~~~ -In file included from mainbb.h:4, - from mainbb.cpp:1: -bb_options.h: At global scope: -bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] - 62 | static const string usege_splash_screen() { - | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp -gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()': -gainLoss.cpp:3980:73: warning: 'AlphaGain' may be used uninitialized [-Wmaybe-uninitialized] - 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); - | ~~~~~~~~~~^~~~~~~~~~~ -gainLoss.cpp:3947:17: note: 'AlphaGain' was declared here - 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; - | ^~~~~~~~~ -gainLoss.cpp:3980:73: warning: 'AlphaLoss' may be used uninitialized [-Wmaybe-uninitialized] - 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); - | ~~~~~~~~~~^~~~~~~~~~~ -gainLoss.cpp:3947:27: note: 'AlphaLoss' was declared here - 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; - | ^~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp -In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, - from gainLossUtils.h:27, - from gainLossUtils.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLossUtils.cpp:19: -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -../../libs/phylogeny/distributionPlusInvariant.h: At global scope: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -In file included from gainLossUtils.cpp:20: -../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' - 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossUtils.cpp: In function 'void printTreeWithValuesAsBP(std::ostream&, tree::TreeNode* const&, Vstring, VVVdouble*, bool)': -gainLossUtils.cpp:72:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] - 72 | if(probs) - | ^ -gainLossUtils.cpp:88:27: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] - 88 | if(probs) - | ^ -gainLossUtils.cpp: In function 'void updateGainBeta(double, std::vector >&, distribution*, distribution*, bool)': -gainLossUtils.cpp:481:17: warning: variable 'normFactor' set but not used [-Wunused-but-set-variable] - 481 | MDOUBLE normFactor; - | ^~~~~~~~~~ -gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': -gainLossUtils.cpp:788:17: warning: unused variable 'scale' [-Wunused-variable] - 788 | MDOUBLE scale; - | ^~~~~ -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; - | ^~~ -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; - | ^~ -gainLoss.cpp: In member function 'void gainLoss::startStochasticProcess()': -gainLoss.cpp:865:83: warning: 'rateDist' may be used uninitialized [-Wmaybe-uninitialized] - 865 | _sp = new stochasticProcess(rateDist,pijAcc,gainLossOptions::_isReversible); - | ^ -gainLoss.cpp:806:23: note: 'rateDist' was declared here - 806 | distribution* rateDist; - | ^~~~~~~~ -ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o -ar: creating libfastml.a -a - fastml.o -a - bbAlg.o -a - bbComputeDownAlg.o -a - bbComputeUpAlg.o -a - bbEvaluateSpecificAV.o -a - bbfindBestAVDynProg.o -a - bbNodeOrderAlg.o -a - bb_options.o -a - bbReport.o -a - computeMarginalReconstruction.o -a - jointNoGamma.o -a - mainbb.o -a - sequenceDataDiff.o -a - suffStatComponentJointNoGamma.o -ranlib libfastml.a -g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml -gainLoss.cpp: In member function 'void gainLoss::startStochasticProcessVec()': -gainLoss.cpp:1124:117: warning: 'rateDist' may be used uninitialized [-Wmaybe-uninitialized] - 1124 | stochasticProcess* sp = new stochasticProcess(rateDist,pijAcc,gainLossOptions::_isReversible); - | ^ -gainLoss.cpp:1105:39: note: 'rateDist' was declared here - 1105 | distribution* rateDist; - | ^~~~~~~~ -make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp -gainLoss.cpp: In member function 'void gainLoss::computeCoEvolutionScoresBasedOnSimulatedData(sequenceContainer&)': -gainLoss.cpp:2484:22: warning: 'countsGL' may be used uninitialized [-Wmaybe-uninitialized] - 2484 | countsGL->run(); - | ~~~~~~~~~~~~~^~ -gainLoss.cpp:2466:26: note: 'countsGL' was declared here - 2466 | computeCountsGL* countsGL; - | ^~~~~~~~ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, @@ -3053,6 +2997,52 @@ optimizeGainLossModel.cpp:85:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] 85 | MDOUBLE sumPijQij; | ^~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp +In file included from bbAlg.h:8, + from mainbb.cpp:5: +bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': +bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] + 14 | const string& _reportFileName; + | ^~~~~~~~~~~~~~~ +bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] + 13 | const int _minNumOfNodesToVisit; + | ^~~~~~~~~~~~~~~~~~~~~ +bbReport.h:10:18: warning: when initialized here [-Wreorder] + 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) + | ^~~~~~~~~~~~~~~~~ +In file included from 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] + 175 | stochasticProcess& _sp; + | ^~~ +../../libs/phylogeny/bestGtrModelParams.h:173:34: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] + 173 | const gammaDistribution* _pProportionDist; + | ^~~~~~~~~~~~~~~~ +../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] + 162 | C_evalGTRParamProportional( const GTRParam param, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()': +gainLoss.cpp:3980:73: warning: 'AlphaGain' may be used uninitialized [-Wmaybe-uninitialized] + 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); + | ~~~~~~~~~~^~~~~~~~~~~ +gainLoss.cpp:3947:17: note: 'AlphaGain' was declared here + 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; + | ^~~~~~~~~ +gainLoss.cpp:3980:73: warning: 'AlphaLoss' may be used uninitialized [-Wmaybe-uninitialized] + 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); + | ~~~~~~~~~~^~~~~~~~~~~ +gainLoss.cpp:3947:27: note: 'AlphaLoss' was declared here + 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; + | ^~~~~~~~~ +In file included from mainbb.h:4, + from mainbb.cpp:1: +bb_options.h: At global scope: +bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] + 62 | static const string usege_splash_screen() { + | ^~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, @@ -3096,7 +3086,13 @@ optimizeGainLossModelVV.cpp:76:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] 76 | MDOUBLE sumPijQij; | ^~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp +gainLoss.cpp: In member function 'void gainLoss::startStochasticProcess()': +gainLoss.cpp:865:83: warning: 'rateDist' may be used uninitialized [-Wmaybe-uninitialized] + 865 | _sp = new stochasticProcess(rateDist,pijAcc,gainLossOptions::_isReversible); + | ^ +gainLoss.cpp:806:23: note: 'rateDist' was declared here + 806 | distribution* rateDist; + | ^~~~~~~~ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, @@ -3151,14 +3147,48 @@ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): | ^~~~~~~~~~~~~ +gainLoss.cpp: In member function 'void gainLoss::startStochasticProcessVec()': +gainLoss.cpp:1124:117: warning: 'rateDist' may be used uninitialized [-Wmaybe-uninitialized] + 1124 | stochasticProcess* sp = new stochasticProcess(rateDist,pijAcc,gainLossOptions::_isReversible); + | ^ +gainLoss.cpp:1105:39: note: 'rateDist' was declared here + 1105 | distribution* rateDist; + | ^~~~~~~~ +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; + | ^~ +gainLoss.cpp: In member function 'void gainLoss::computeCoEvolutionScoresBasedOnSimulatedData(sequenceContainer&)': +gainLoss.cpp:2484:22: warning: 'countsGL' may be used uninitialized [-Wmaybe-uninitialized] + 2484 | countsGL->run(); + | ~~~~~~~~~~~~~^~ +gainLoss.cpp:2466:26: note: 'countsGL' was declared here + 2466 | computeCountsGL* countsGL; + | ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp -gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': -gainLoss.cpp:1195:24: warning: 'pDm' may be used uninitialized [-Wmaybe-uninitialized] - 1195 | delete pDm; - | ^~~ -gainLoss.cpp:1173:33: note: 'pDm' was declared here - 1173 | distanceMethod* pDm; - | ^~~ +ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o +ar: creating libfastml.a +a - fastml.o +a - bbAlg.o +a - bbComputeDownAlg.o +a - bbComputeUpAlg.o +a - bbEvaluateSpecificAV.o +a - bbfindBestAVDynProg.o +a - bbNodeOrderAlg.o +a - bb_options.o +a - bbReport.o +a - computeMarginalReconstruction.o +a - jointNoGamma.o +a - mainbb.o +a - sequenceDataDiff.o +a - suffStatComponentJointNoGamma.o +ranlib libfastml.a +g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml +make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from siteSpecificGL.cpp:23: @@ -3185,22 +3215,6 @@ 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp -In file included from /usr/include/c++/14/vector:72, - from ../../libs/phylogeny/definitions.h:18, - from siteSpecificGL.h:22, - from siteSpecificGL.cpp:18: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void computeEB_EXP_siteSpecificGL(int, const sequenceContainer&, const std::vector >&, const tree&, const distribution*, const distribution*, const distribution*, Vdouble&, double&, double&, double&, double&, double, VVVdouble&, unObservableData*)' at siteSpecificGL.cpp:102:19: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, @@ -3227,6 +3241,22 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp +In file included from /usr/include/c++/14/vector:72, + from ../../libs/phylogeny/definitions.h:18, + from siteSpecificGL.h:22, + from siteSpecificGL.cpp:18: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void computeEB_EXP_siteSpecificGL(int, const sequenceContainer&, const std::vector >&, const tree&, const distribution*, const distribution*, const distribution*, Vdouble&, double&, double&, double&, double&, double, VVVdouble&, unObservableData*)' at siteSpecificGL.cpp:102:19: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp In file included from gainLoss.h:30, from gainLossProject.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] @@ -3288,7 +3318,6 @@ 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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp In file included from gainLoss.h:30, from gainLossOptimizer.h:24, from gainLossOptimizer.cpp:17: @@ -3317,6 +3346,7 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp In file included from gainLossOptimizer.cpp:20: bblLS.h: At global scope: bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] @@ -3421,15 +3451,14 @@ gainLossOptimizer.cpp:623:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] 623 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp +gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': +gainLoss.cpp:1195:24: warning: 'pDm' may be used uninitialized [-Wmaybe-uninitialized] + 1195 | delete pDm; + | ^~~ +gainLoss.cpp:1173:33: note: 'pDm' was declared here + 1173 | distanceMethod* pDm; + | ^~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp -gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': -gainLossOptimizer.cpp:833:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] - 833 | return res; - | ^~~ -gainLossOptimizer.cpp:820:43: note: 'res' was declared here - 820 | gainLossOptions::distributionType res; - | ^~~ In file included from gainLoss.h:30, from rate4siteGL.h:24, from rate4siteGL.cpp:17: @@ -3475,6 +3504,14 @@ rate4siteGL.cpp:152:13: warning: unused variable 'precisionLow' [-Wunused-variable] 152 | int precisionLow = 3; | ^~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp +gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': +gainLossOptimizer.cpp:833:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] + 833 | return res; + | ^~~ +gainLossOptimizer.cpp:820:43: note: 'res' was declared here + 820 | gainLossOptions::distributionType res; + | ^~~ In file included from /usr/include/c++/14/vector:72, from ../../libs/phylogeny/definitions.h:18, from rate4siteGL.h:22: @@ -3488,9 +3525,6 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp In file included from gainLoss.h:30, from computeCountsGL.h:24, from computeCountsGL.cpp:17: @@ -3519,6 +3553,7 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, VVdouble&, double, bool)': computeCountsGL.h:104:14: warning: 'computeCountsGL::_tr' will be initialized after [-Wreorder] 104 | tree _tr; @@ -3585,38 +3620,10 @@ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from gainLoss.h:30, - from gainLoss4site.h:24, - from gainLoss4site.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -In file included from gainLossUtils.h:27, - from gainLossModel.h:27, - from gainLoss.h:35: -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 | ^~~~~~~~~~~~~ -gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] - 58 | virtual gainLossModel& operator=(const gainLossModel &other); - | ^~~~~~~~ -gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' - 124 | class gainLossModelNonReversible : public gainLossModel { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': -gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] - 186 | MDOUBLE _loss; // _Q[1][0] - | ^~~~~ -gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] - 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) - | ^ -gainLossModel.h:127:18: warning: when initialized here [-Wreorder] - 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': computeCorrelations.cpp:408:29: warning: unused variable 'isHigherNminReducedFreqOfHighCorr' [-Wunused-variable] 408 | int isHigherNminReducedFreqOfHighCorr = false; @@ -3672,28 +3679,10 @@ computeCorrelations.cpp:1300:14: warning: variable 'it_siteB' set but not used [-Wunused-but-set-variable] 1300 | it_B it_siteB = it_siteA->second.begin(); | ^~~~~~~~ -gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::string&, unObservableData*, double)': -gainLoss4site.h:68:14: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] - 68 | tree _tr; - | ^~~ -gainLoss4site.h:61:45: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] - 61 | vector > _spVVec; //save stochasticProcess for each category - | ^~~~~~~ -gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] - 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, - | ^~~~~~~~~~~~~ -gainLoss4site.h:79:27: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] - 79 | unObservableData* _unObservableData_p; // - | ^~~~~~~~~~~~~~~~~~~ -gainLoss4site.h:78:17: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] - 78 | MDOUBLE _alphaConf; - | ^~~~~~~~~~ -gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] - 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, - | ^~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp In file included from gainLoss.h:30, - from simulateChangesAlongTree.cpp:20: + 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); | ^~~~~~~~ @@ -3719,6 +3708,25 @@ 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::string&, unObservableData*, double)': +gainLoss4site.h:68:14: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] + 68 | tree _tr; + | ^~~ +gainLoss4site.h:61:45: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] + 61 | vector > _spVVec; //save stochasticProcess for each category + | ^~~~~~~ +gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] + 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, + | ^~~~~~~~~~~~~ +gainLoss4site.h:79:27: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] + 79 | unObservableData* _unObservableData_p; // + | ^~~~~~~~~~~~~~~~~~~ +gainLoss4site.h:78:17: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] + 78 | MDOUBLE _alphaConf; + | ^~~~~~~~~~ +gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] + 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, + | ^~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from gainLoss.h:75: @@ -3798,6 +3806,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2137 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp In file included from /usr/include/c++/14/map:62, from ../../libs/phylogeny/njConstrain.h:6, from ../../libs/phylogeny/nj.h:11, @@ -3830,7 +3839,6 @@ /usr/include/c++/14/bits/stl_algo.h:2135:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h:2135:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h:2135:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp In function 'std::pair<_FIter, _FIter> std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', inlined from 'void computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMap(VVVdouble&, VVVVdouble&, VVVdouble&)' at computeCorrelations.cpp:848:26: /usr/include/c++/14/bits/stl_algo.h:2135:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3850,7 +3858,7 @@ 2137 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:30, - from simulateOnePos.cpp:32: + 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); | ^~~~~~~~ @@ -3885,42 +3893,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from simulateOnePos.cpp:18: -simulateOnePos.h: In constructor 'simulateOnePos::simulateOnePos(std::string, std::ostream*, std::ostream*, int, std::string, double, double, bool, stochasticProcess*, tree*, Vdouble*, Vdouble*)': -simulateOnePos.h:72:14: warning: 'simulateOnePos::_simulateNullModel' will be initialized after [-Wreorder] - 72 | bool _simulateNullModel; - | ^~~~~~~~~~~~~~~~~~ -simulateOnePos.h:63:13: warning: 'int simulateOnePos::_simNum' [-Wreorder] - 63 | int _simNum; - | ^~~~~~~ -simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] - 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile - | ^~~~~~~~~~~~~~ -simulateOnePos.h:65:17: warning: 'simulateOnePos::_theta' will be initialized after [-Wreorder] - 65 | MDOUBLE _theta; - | ^~~~~~ -simulateOnePos.h:64:17: warning: 'double simulateOnePos::_sumGainLoss' [-Wreorder] - 64 | MDOUBLE _sumGainLoss; - | ^~~~~~~~~~~~ -simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] - 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile - | ^~~~~~~~~~~~~~ -simulateOnePos.h:75:18: warning: 'simulateOnePos::_freq_cpN' will be initialized after [-Wreorder] - 75 | Vdouble* _freq_cpN; - | ^~~~~~~~~ -simulateOnePos.h:69:18: warning: 'std::ostream* simulateOnePos::_simulatedEvents' [-Wreorder] - 69 | ostream *_simulatedEvents; - | ^~~~~~~~~~~~~~~~ -simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] - 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile - | ^~~~~~~~~~~~~~ -simulateOnePos.cpp: In member function 'void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::string)': -simulateOnePos.cpp:181:30: warning: unused variable 'isRevers' [-Wunused-variable] - 181 | bool isRevers = false; - | ^~~~~~~~ -simulateOnePos.cpp:202:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] - 202 | MDOUBLE sumQii = 1.0; - | ^~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from 'void computeCorrelations::produceSortedVectorsOfAllCorrelations(Vdouble&)' at computeCorrelations.cpp:294:7: @@ -4048,6 +4021,70 @@ /usr/include/c++/14/bits/stl_algo.h:4772:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 4772 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from gainLoss.h:30, + from simulateOnePos.cpp:32: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +In file included from gainLossUtils.h:27, + from gainLossModel.h:27, + from gainLoss.h:35: +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] + 58 | virtual gainLossModel& operator=(const gainLossModel &other); + | ^~~~~~~~ +gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' + 124 | class gainLossModelNonReversible : public gainLossModel { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': +gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] + 186 | MDOUBLE _loss; // _Q[1][0] + | ^~~~~ +gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] + 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) + | ^ +gainLossModel.h:127:18: warning: when initialized here [-Wreorder] + 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from simulateOnePos.cpp:18: +simulateOnePos.h: In constructor 'simulateOnePos::simulateOnePos(std::string, std::ostream*, std::ostream*, int, std::string, double, double, bool, stochasticProcess*, tree*, Vdouble*, Vdouble*)': +simulateOnePos.h:72:14: warning: 'simulateOnePos::_simulateNullModel' will be initialized after [-Wreorder] + 72 | bool _simulateNullModel; + | ^~~~~~~~~~~~~~~~~~ +simulateOnePos.h:63:13: warning: 'int simulateOnePos::_simNum' [-Wreorder] + 63 | int _simNum; + | ^~~~~~~ +simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] + 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile + | ^~~~~~~~~~~~~~ +simulateOnePos.h:65:17: warning: 'simulateOnePos::_theta' will be initialized after [-Wreorder] + 65 | MDOUBLE _theta; + | ^~~~~~ +simulateOnePos.h:64:17: warning: 'double simulateOnePos::_sumGainLoss' [-Wreorder] + 64 | MDOUBLE _sumGainLoss; + | ^~~~~~~~~~~~ +simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] + 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile + | ^~~~~~~~~~~~~~ +simulateOnePos.h:75:18: warning: 'simulateOnePos::_freq_cpN' will be initialized after [-Wreorder] + 75 | Vdouble* _freq_cpN; + | ^~~~~~~~~ +simulateOnePos.h:69:18: warning: 'std::ostream* simulateOnePos::_simulatedEvents' [-Wreorder] + 69 | ostream *_simulatedEvents; + | ^~~~~~~~~~~~~~~~ +simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] + 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile + | ^~~~~~~~~~~~~~ +simulateOnePos.cpp: In member function 'void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::string)': +simulateOnePos.cpp:181:30: warning: unused variable 'isRevers' [-Wunused-variable] + 181 | bool isRevers = false; + | ^~~~~~~~ +simulateOnePos.cpp:202:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] + 202 | MDOUBLE sumQii = 1.0; + | ^~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from bblLS.h:27, @@ -4099,7 +4136,35 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp +In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, + from gainLossUtils.h:27, + from sankoffReconstructGL.h:29, + from sankoffReconstructGL.cpp:17: +../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] + 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); + | ^~~~~~~~ +../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' + 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)': +sankoffReconstructGL.h:85:16: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] + 85 | string _outDir; + | ^~~~~~~ +sankoffReconstructGL.h:84:17: warning: 'double sankoffReconstructGL::_costMatrixGainLossRatio' [-Wreorder] + 84 | MDOUBLE _costMatrixGainLossRatio; + | ^~~~~~~~~~~~~~~~~~~~~~~~ +sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] + 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): + | ^~~~~~~~~~~~~~~~~~~~ +sankoffReconstructGL.h:84:17: warning: 'sankoffReconstructGL::_costMatrixGainLossRatio' will be initialized after [-Wreorder] + 84 | MDOUBLE _costMatrixGainLossRatio; + | ^~~~~~~~~~~~~~~~~~~~~~~~ +sankoffReconstructGL.h:83:17: warning: 'double sankoffReconstructGL::_distanceFromRootForRecent' [-Wreorder] + 83 | MDOUBLE _distanceFromRootForRecent; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] + 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): + | ^~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)' at computeCorrelations.cpp:1323:93: /usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 @@ -4167,35 +4232,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, - from gainLossUtils.h:27, - from sankoffReconstructGL.h:29, - from sankoffReconstructGL.cpp:17: -../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] - 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); - | ^~~~~~~~ -../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' - 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)': -sankoffReconstructGL.h:85:16: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] - 85 | string _outDir; - | ^~~~~~~ -sankoffReconstructGL.h:84:17: warning: 'double sankoffReconstructGL::_costMatrixGainLossRatio' [-Wreorder] - 84 | MDOUBLE _costMatrixGainLossRatio; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] - 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): - | ^~~~~~~~~~~~~~~~~~~~ -sankoffReconstructGL.h:84:17: warning: 'sankoffReconstructGL::_costMatrixGainLossRatio' will be initialized after [-Wreorder] - 84 | MDOUBLE _costMatrixGainLossRatio; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -sankoffReconstructGL.h:83:17: warning: 'double sankoffReconstructGL::_distanceFromRootForRecent' [-Wreorder] - 83 | MDOUBLE _distanceFromRootForRecent; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] - 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): - | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:72, + from ../../libs/phylogeny/definitions.h:18, + from ../../libs/phylogeny/tree.h:6, + from sankoffReconstructGL.h:23: +/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double sankoffReconstructGL::traverseDownMP(VVdouble&, std::vector > >&, VVint&, VVdouble&)' at sankoffReconstructGL.cpp:368:23: +/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': computeCorrelations.cpp:505:33: warning: 'expextedFreq' may be used uninitialized [-Wmaybe-uninitialized] 505 | if(freqOfHighCorr>expextedFreq && freqOfHighCorr >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from ../../libs/phylogeny/definitions.h:18, - from ../../libs/phylogeny/tree.h:6, - from sankoffReconstructGL.h:23: -/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double sankoffReconstructGL::traverseDownMP(VVdouble&, std::vector > >&, VVint&, VVdouble&)' at sankoffReconstructGL.cpp:368:23: -/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void sankoffReconstructGL::traverseUpMP(VVdouble&, std::vector > >&)' at sankoffReconstructGL.cpp:315:20: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -4288,7 +4324,7 @@ 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 -j3 test + make -j4 test make[1]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make test cd programs;make test @@ -4297,22 +4333,22 @@ make[2]: Entering directory '/build/reproducible-path/fastml-3.11/programs' cd fastml && make test cd gainLoss && make test -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' -cd tests; make -k test -make[4]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny/tests' -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. split_test.cpp ../libEvolTree.a -lEvolTree -o split_test +cd indelCoder && make test 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/fastml' +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' +cd tests; make -k test make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' if [ -d tests ] ; then cd tests && make -k ; fi -cd indelCoder && make test -make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. splitMap_test.cpp ../libEvolTree.a -lEvolTree -o splitMap_test make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' if [ -d tests ] ; then cd tests && make -k ; fi +make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' +make[4]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny/tests' +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. split_test.cpp ../libEvolTree.a -lEvolTree -o split_test make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. splitMap_test.cpp ../libEvolTree.a -lEvolTree -o splitMap_test g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqTheDistBetweenThem-3.cpp ../libEvolTree.a -lEvolTree -o given2seqTheDistBetweenThem-3 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistBetweenThem.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistBetweenThem g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. checkTreeLikelihoodGivenBranches.cpp ../libEvolTree.a -lEvolTree -o checkTreeLikelihoodGivenBranches @@ -4325,18 +4361,18 @@ ./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp ./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp -./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp -./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp ./doubleRep > doubleRep.out.tmp -./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp diff split_test.out.tmp split_test.out.standard diff splitMap_test.out.tmp splitMap_test.out.standard diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard +diff doubleRep.out.tmp doubleRep.out.standard +./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard +./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard -diff doubleRep.out.tmp doubleRep.out.standard +./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp diff readTreeWithComments.out.tmp readTreeWithComments.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' @@ -4347,7 +4383,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/fastml/ - make -j3 install DESTDIR=/build/reproducible-path/fastml-3.11/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + make -j4 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' @@ -4361,18 +4397,18 @@ cd fastml && make install cd gainLoss && make install cd indelCoder && make install -make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' -mkdir -p ../../bin -cp indelCoder ../../bin/indelCoder make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' mkdir -p ../../bin +cp fastml ../../bin/fastml make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss -cp fastml ../../bin/fastml +make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' +mkdir -p ../../bin +cp indelCoder ../../bin/indelCoder +make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' -make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' make[1]: Leaving directory '/build/reproducible-path/fastml-3.11' dh_install @@ -4393,15 +4429,15 @@ diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged +dpkg-shlibdeps: warning: debian/fastml/usr/bin/gainLoss contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/fastml/usr/bin/indelCoder contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/fastml/usr/bin/fastml contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/fastml/usr/bin/gainLoss contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.11-4_armhf.deb'. dpkg-deb: building package 'fastml' in '../fastml_3.11-4_armhf.deb'. +dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.11-4_armhf.deb'. dpkg-genbuildinfo --build=binary -O../fastml_3.11-4_armhf.buildinfo dpkg-genchanges --build=binary -O../fastml_3.11-4_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4409,12 +4445,14 @@ 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/21011/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/21011/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/9244 and its subdirectories -I: Current time: Sun Jan 19 21:50:55 -12 2025 -I: pbuilder-time-stamp: 1737366655 +I: removing directory /srv/workspace/pbuilder/21011 and its subdirectories +I: Current time: Mon Jan 20 23:58:44 +14 2025 +I: pbuilder-time-stamp: 1737367124