I: pbuilder: network access will be disabled during build
I: Current time: Tue Feb 25 18:25:26 -12 2025
I: pbuilder-time-stamp: 1740551126
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [fastml_3.11-4.dsc]
I: copying [./fastml_3.11.orig.tar.gz]
I: copying [./fastml_3.11-4.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./fastml_3.11-4.dsc: unsupported subcommand
dpkg-source: info: extracting fastml in fastml-3.11
dpkg-source: info: unpacking fastml_3.11.orig.tar.gz
dpkg-source: info: unpacking fastml_3.11-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying gcc_5.patch
dpkg-source: info: applying fix_makefile4test.patch
dpkg-source: info: applying fix_intall_target.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying change_to_tests_dir_only_if_existing.patch
dpkg-source: info: applying skip_failing_tests.patch
dpkg-source: info: applying remove-template-depth.patch
dpkg-source: info: applying cross.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/18634/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='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='fab055155e7846f3a6ae27a6f1a7f019'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='18634'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.WorESvhL/pbuilderrc_BuSQ --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.WorESvhL/b1 --logfile b1/build.log fastml_3.11-4.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://46.16.76.132:3128'
I: uname -a
Linux ionos12-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/18634/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19786 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.8 MB of archives. After unpacking 78.2 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
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Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-4 [96.4 kB]
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Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Fetched 20.8 MB in 0s (53.0 MB/s)
Preconfiguring packages ...
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(Reading database ... 19786 files and directories currently installed.)
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Setting up libmagic-mgc (1:5.45-3+b1) ...
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Setting up libunistring5:i386 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
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Initializing package states...
Writing extended state information...
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
dpkg-buildpackage: info: source package fastml
dpkg-buildpackage: info: source version 3.11-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/fastml-3.11'
dh_auto_clean
make -j11 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
make[4]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny'
rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o
cd gainLoss && make clean
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/fastml'
rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o
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]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml'
make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder'
rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o
make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss'
make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder'
make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs'
make[2]: Leaving directory '/build/reproducible-path/fastml-3.11'
rm -f libs/phylogeny/make.dep \
programs/fastml/make.dep \
programs/gainLoss/make.dep \
programs/indelCoder/make.dep
rm -rf bin
find libs/phylogeny/tests -type f -executable -delete
make[1]: Leaving directory '/build/reproducible-path/fastml-3.11'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j11 "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'
cd phylogeny && make all
make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny'
making depend
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o AddLog.o AddLog.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiProp.o NNiProp.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiSep.o NNiSep.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Nni.o Nni.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o aaJC.o aaJC.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTrees.o allTrees.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp
bestAlphaManyTrees.cpp: In function 'void bestAlpha::optimizeAlphaNG_EM_PROP_n_alpha(tree&, std::vector<sequenceContainer>&, std::vector<stochasticProcess>&, const std::vector<std::vector<double>*>*, std::vector<double>&, double&, int, double)':
bestAlphaManyTrees.cpp:184:17: warning: variable 'ax' set but not used [-Wunused-but-set-variable]
184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha
| ^~
bestAlphaManyTrees.cpp:184:20: warning: variable 'bx' set but not used [-Wunused-but-set-variable]
184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha
| ^~
bestAlphaManyTrees.cpp:184:23: warning: variable 'cx' set but not used [-Wunused-but-set-variable]
184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha
| ^~
bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)':
bestAlpha.cpp:371:17: warning: variable 'oldA' set but not used [-Wunused-but-set-variable]
371 | MDOUBLE oldA=0;
| ^~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlg.o computeUpAlg.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp
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]
57 | VVVdouble _LpostPerSpPerCat; // _LpostPerSpPerCat[sp][rateCat][pos]
| ^~~~~~~~~~~~~~~~~
computeSubstitutionCounts.h:53:13: warning: 'int computeSubstitutionCounts::_simulationsIterNum' [-Wreorder]
53 | int _simulationsIterNum;
| ^~~~~~~~~~~~~~~~~~~
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):
| ^~~~~~~~~~~~~~~~~~~~~~~~~
computeSubstitutionCounts.h:54:17: warning: 'computeSubstitutionCounts::_probCutOffSum' will be initialized after [-Wreorder]
54 | MDOUBLE _probCutOffSum;
| ^~~~~~~~~~~~~~
computeSubstitutionCounts.h:52:14: warning: 'bool computeSubstitutionCounts::_isSilent' [-Wreorder]
52 | bool _isSilent;
| ^~~~~~~~~
computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder]
15 | computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent):
| ^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp
In file included from /usr/include/c++/14/iostream:41,
from readTree.h:6,
from tree.h:7,
from computeDownAlg.h:7,
from computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:2:
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3:
/usr/include/c++/14/ostream:232:25: warning: 'Down' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)':
computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:25: note: 'Down' was declared here
55 | MDOUBLE resDXY, Down, Up, pij;
| ^~~~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3:
/usr/include/c++/14/ostream:232:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)':
computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:31: note: 'Up' was declared here
55 | MDOUBLE resDXY, Down, Up, pij;
| ^~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3:
/usr/include/c++/14/ostream:232:25: warning: 'pij' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)':
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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3,
inlined from 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:39:108:
/usr/include/c++/14/ostream:232:25: warning: 'Down' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)':
computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:25: note: 'Down' was declared here
55 | MDOUBLE resDXY, Down, Up, pij;
| ^~~~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3,
inlined from 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:39:108:
/usr/include/c++/14/ostream:232:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)':
computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:31: note: 'Up' was declared here
55 | MDOUBLE resDXY, Down, Up, pij;
| ^~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3,
inlined from 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:39:108:
/usr/include/c++/14/ostream:232:25: warning: 'pij' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)':
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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp
In file included from fromCountTableComponentToDistancePropEB.cpp:3:
fromCountTableComponentToDistancePropEB.h: In constructor 'fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB(const std::vector<std::vector<countTableComponentGamProportional> >&, int, multipleStochasticProcess*, const gammaDistribution*, double, double)':
fromCountTableComponentToDistancePropEB.h:29:19: warning: 'fromCountTableComponentToDistancePropEB::_nodeID' will be initialized after [-Wreorder]
29 | const int _nodeID;
| ^~~~~~~
fromCountTableComponentToDistancePropEB.h:28:34: warning: 'const gammaDistribution* fromCountTableComponentToDistancePropEB::_pProportionDist' [-Wreorder]
28 | const gammaDistribution* _pProportionDist;
| ^~~~~~~~~~~~~~~~
fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder]
6 | fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp
In member function 'virtual void generalGammaDistribution::setGammaParameters(int, double, double)',
inlined from 'generalGammaDistribution::generalGammaDistribution(double, double, int)' at generalGammaDistribution.cpp:34:20:
generalGammaDistribution.cpp:56:26: warning: '*this.generalGammaDistribution::_alpha' is used uninitialized [-Wuninitialized]
56 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories()))
| ^~~~~~
generalGammaDistribution.cpp:56:49: warning: '*this.generalGammaDistribution::_beta' may be used uninitialized [-Wmaybe-uninitialized]
56 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories()))
| ^~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp
goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)':
goldmanYangModel.cpp:8:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self]
8 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV):
| ^~~~~~~~~~~~~~~~
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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.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,
| ~~~~~~~~~~^~~~~~~~~~
270 | C_evalLikeDist_d(ctc,_sp),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
271 | C_evalLikeDist_d2(ctc,_sp),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
272 | tol,
| ~~~~
273 | 100,
| ~~~~
274 | zeroFound);// max it for NR;
| ~~~~~~~~~~
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 -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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp
numRec.cpp:306:2: warning: "/*" within comment [-Wcomment]
306 | //* for (i=1;i<n;i++) e[i-1]=e[i];
numRec.cpp:307:2: warning: "/*" within comment [-Wcomment]
307 | //* e[n-1]=0.0;
numRec.cpp:308:2: warning: "/*" within comment [-Wcomment]
308 | //* e.push_back(0);//since in my algorithm I return an n-1 sized e
In file included from /usr/include/c++/14/cassert:44,
from njConstrain.cpp:4:
njConstrain.cpp: In function 'tree::TreeNode* joinNodesToSubtree(tree&, tree::TreeNode*&, tree::TreeNode*&)':
njConstrain.cpp:92:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
92 | assert (k=fatherNode->getNumberOfSons()+2); // both s1 and s2 should have been skiped
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
likelihoodComputation.cpp: In function 'double likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(const tree&, const sequenceContainer&, const stochasticProcess&, const Vdouble*, unObservableData*)':
likelihoodComputation.cpp:43:45: warning: 'LforMissingData' may be used uninitialized [-Wmaybe-uninitialized]
43 | LofPos = LofPos / (1- LforMissingData);
| ~~^~~~~~~~~~~~~~~~~~
likelihoodComputation.cpp:27:17: note: 'LforMissingData' was declared here
27 | MDOUBLE LforMissingData;
| ^~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequence.o sequence.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp
sequence.cpp: In constructor 'sequence::sequence(const sequence&, const alphabet*)':
sequence.cpp:76:42: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
76 | || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0))
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.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;
| ^~~~~~
sequenceContainer.cpp: In member function 'void sequenceContainer::removeGapPositionsAllSeqs()':
sequenceContainer.cpp:199:14: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable]
199 | bool gapCol;
| ^~~~~~
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();
| ^~~
sequenceContainer.cpp: In member function 'std::vector<std::__cxx11::basic_string<char> > sequenceContainer::getSeqNamesThatMatchPos(int, char)':
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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp
treeUtil.cpp: In function 'std::vector<tree> getNexusTreesFromFile(const std::string&)':
treeUtil.cpp:371:32: warning: variable 'itStrStart' set but not used [-Wunused-but-set-variable]
371 | string::const_iterator itStrStart = it->begin();
| ^~~~~~~~~~
treeUtil.cpp:372:32: warning: variable 'itStrEnd' set but not used [-Wunused-but-set-variable]
372 | string::const_iterator itStrEnd = it->end();
| ^~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp
In file included from distanceBasedSeqs2Tree.cpp:12:
bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)':
bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder]
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,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp
In file included from pairwiseGammaDistance.h:6,
from pairwiseGammaDistance.cpp:3:
likeDist.h:51:19: warning: 'virtual const double likeDist::giveDistance(const sequence&, const sequence&, const std::vector<double>*, double*) const' was hidden [-Woverloaded-virtual=]
51 | const MDOUBLE giveDistance(const sequence& s1,
| ^~~~~~~~~~~~
pairwiseGammaDistance.h:32:19: note: by 'const double pairwiseGammaDistance::giveDistance(const sequence&, const sequence&, const std::vector<double>*, double*, double*) const'
32 | const MDOUBLE giveDistance(const sequence& s1,
| ^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.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]
54 | vector<MDOUBLE> _boundary;
| ^~~~~~~~~
betaDistribution.h:47:17: warning: 'double betaDistribution::_alpha' [-Wreorder]
47 | MDOUBLE _alpha;
| ^~~~~~
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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp
In member function 'virtual void betaDistribution::setBetaParameters(int, double, double)',
inlined from 'betaDistribution::betaDistribution(double, double, int, discretizationType)' at betaDistribution.cpp:36:19:
betaDistribution.cpp:72:26: warning: '*this.betaDistribution::_alpha' is used uninitialized [-Wuninitialized]
72 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories()))
| ^~~~~~
betaDistribution.cpp:72:49: warning: '*this.betaDistribution::_beta' may be used uninitialized [-Wmaybe-uninitialized]
72 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories()))
| ^~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp
In file included from computeJumps.cpp:1:
computeJumps.h: In constructor 'computeJumps::gFunc::gFunc(double, double, double)':
computeJumps.h:59:25: warning: 'computeJumps::gFunc::_Lambda2' will be initialized after [-Wreorder]
59 | MDOUBLE _Lambda2;
| ^~~~~~~~
computeJumps.h:57:25: warning: 'double computeJumps::gFunc::_r' [-Wreorder]
57 | MDOUBLE _r;
| ^~
computeJumps.cpp:256:1: warning: when initialized here [-Wreorder]
256 | computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r)
| ^~~~~~~~~~~~
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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp
suffStatGammaMixture.cpp: In member function 'void suffStatGammaMixture::computeStatistics()':
suffStatGammaMixture.cpp:123:33: warning: variable 'Exp_Rk' set but not used [-Wunused-but-set-variable]
123 | MDOUBLE Exp_Rk, Exp_LogRk, sum;
| ^~~~~~
suffStatGammaMixture.cpp: In member function 'double suffStatGammaMixture::computeQ()':
suffStatGammaMixture.cpp:224:25: warning: unused variable 'first' [-Wunused-variable]
224 | MDOUBLE first = _MkVec[comp] * log(P_k);
| ^~~~~
suffStatGammaMixture.cpp:225:25: warning: unused variable 'second' [-Wunused-variable]
225 | MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k);
| ^~~~~~
suffStatGammaMixture.cpp:226:25: warning: unused variable 'third' [-Wunused-variable]
226 | MDOUBLE third = -_MkVec[comp] * gammln(alpha_k);
| ^~~~~
suffStatGammaMixture.cpp:227:25: warning: unused variable 'fourth' [-Wunused-variable]
227 | MDOUBLE fourth = -_AkVec[comp]*beta_k;
| ^~~~~~
suffStatGammaMixture.cpp:228:25: warning: unused variable 'fifth' [-Wunused-variable]
228 | MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0);
| ^~~~~
suffStatGammaMixture.cpp:216:17: warning: variable 'res2' set but not used [-Wunused-but-set-variable]
216 | MDOUBLE res2 = 0.0;
| ^~~~
In file included from GamMixtureOptimizer.cpp:3:
optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const':
optGammaMixtureEM.h:76:25: warning: unused variable 'res1' [-Wunused-variable]
76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6)));
| ^~~~
optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const':
optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable]
87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10)));
| ^~~~~~~~
In file included from optGammaMixtureEM.cpp:1:
optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const':
optGammaMixtureEM.h:76:25: warning: unused variable 'res1' [-Wunused-variable]
76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6)));
| ^~~~
optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const':
optGammaMixtureEM.h:87:25: warning: unused variable 'debugRes' [-Wunused-variable]
87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10)));
| ^~~~~~~~
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;
| ^
mixtureDistribution.cpp:210:13: note: 'componentNum' was declared here
210 | int componentNum, categoryInComponent, totalCat = 0;
| ^~~~~~~~~~~~
mixtureDistribution.cpp:221:48: warning: 'categoryInComponent' may be used uninitialized [-Wmaybe-uninitialized]
221 | return _components[componentNum]->rates(categoryInComponent) * _globalRate;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
mixtureDistribution.cpp:210:27: note: 'categoryInComponent' was declared here
210 | int componentNum, categoryInComponent, totalCat = 0;
| ^~~~~~~~~~~~~~~~~~~
In file included from mixtureDistribution.cpp:1:
In member function 'const double mixtureDistribution::getComponentProb(int) const',
inlined from 'virtual const double mixtureDistribution::ratesProb(int) const' at mixtureDistribution.cpp:239:26:
mixtureDistribution.h:40:102: warning: 'componentNum' may be used uninitialized [-Wmaybe-uninitialized]
40 | const MDOUBLE getComponentProb(int componentNum) const {return _componentsWeight[componentNum] / _totalWeight;}
| ^
mixtureDistribution.cpp: In member function 'virtual const double mixtureDistribution::ratesProb(int) const':
mixtureDistribution.cpp:228:13: note: 'componentNum' was declared here
228 | int componentNum, categoryInComponent, totalCat = 0;
| ^~~~~~~~~~~~
mixtureDistribution.cpp:239:86: warning: 'categoryInComponent' may be used uninitialized [-Wmaybe-uninitialized]
239 | return getComponentProb(componentNum) * _components[componentNum]->ratesProb(categoryInComponent);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
mixtureDistribution.cpp:228:27: note: 'categoryInComponent' was declared here
228 | int componentNum, categoryInComponent, totalCat = 0;
| ^~~~~~~~~~~~~~~~~~~
In file included from seqeuncesFilter.h:6,
from seqeuncesFilter.cpp:1:
In member function 'const sequence& sequenceContainer::operator[](int) const',
inlined from 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)' at seqeuncesFilter.cpp:175:16:
sequenceContainer.h:31:88: warning: 'refID' may be used uninitialized [-Wmaybe-uninitialized]
31 | const sequence& operator[](const int id) const {return _seqDataVec[_id2place[id]];}
| ^
seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)':
seqeuncesFilter.cpp:165:13: note: 'refID' was declared here
165 | int refID;
| ^~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp
In file included from /usr/include/i386-linux-gnu/c++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/vector:63,
from definitions.h:18,
from mixtureDistribution.h:11:
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<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]' at /usr/include/c++/14/bits/alloc_traits.h:575:17,
inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator<generalGammaDistribution*>]' at /usr/include/c++/14/bits/stl_vector.h:1288:30,
inlined from 'mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)' at mixtureDistribution.cpp:52:24:
/usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'pComp' may be used uninitialized [-Wmaybe-uninitialized]
191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mixtureDistribution.cpp: In constructor 'mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)':
mixtureDistribution.cpp:40:43: note: 'pComp' declared here
40 | generalGammaDistribution* pComp;
| ^~~~~
In file included from /usr/include/c++/14/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator<generalGammaDistribution*>]',
inlined from 'mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)' at mixtureDistribution.cpp:52:24:
/usr/include/c++/14/bits/stl_vector.h:1294:28: warning: 'pComp' may be used uninitialized [-Wmaybe-uninitialized]
1294 | _M_realloc_append(__x);
| ~~~~~~~~~~~~~~~~~^~~~~
In file included from /usr/include/c++/14/vector:72:
/usr/include/c++/14/bits/vector.tcc: In constructor 'mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)':
/usr/include/c++/14/bits/vector.tcc:581:7: note: by argument 2 of type 'generalGammaDistribution* const&' to 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*; _Alloc = std::allocator<generalGammaDistribution*>]' declared here
581 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
mixtureDistribution.cpp:40:43: note: 'pComp' declared here
40 | generalGammaDistribution* pComp;
| ^~~~~
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<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]' at /usr/include/c++/14/bits/alloc_traits.h:575:17,
inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator<generalGammaDistribution*>]' at /usr/include/c++/14/bits/stl_vector.h:1288:30,
inlined from 'mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)' at mixtureDistribution.cpp:84:24:
/usr/include/c++/14/bits/new_allocator.h:191:11: warning: 'pComp' may be used uninitialized [-Wmaybe-uninitialized]
191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mixtureDistribution.cpp: In constructor 'mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)':
mixtureDistribution.cpp:72:43: note: 'pComp' declared here
72 | generalGammaDistribution* pComp;
| ^~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator<generalGammaDistribution*>]',
inlined from 'mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)' at mixtureDistribution.cpp:84:24:
/usr/include/c++/14/bits/stl_vector.h:1294:28: warning: 'pComp' may be used uninitialized [-Wmaybe-uninitialized]
1294 | _M_realloc_append(__x);
| ~~~~~~~~~~~~~~~~~^~~~~
/usr/include/c++/14/bits/vector.tcc: In constructor 'mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)':
/usr/include/c++/14/bits/vector.tcc:581:7: note: by argument 2 of type 'generalGammaDistribution* const&' to 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*; _Alloc = std::allocator<generalGammaDistribution*>]' declared here
581 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o integerAlphabet.o integerAlphabet.cpp
In file included from gtrModel.cpp:1:
gtrModel.h: In constructor 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)':
gtrModel.h:54:17: warning: 'gtrModel::_g2t' will be initialized after [-Wreorder]
54 | MDOUBLE _g2t;
| ^~~~
gtrModel.h:47:17: warning: 'Vdouble gtrModel::_freq' [-Wreorder]
47 | Vdouble _freq;
| ^~~~~
gtrModel.cpp:5:1: warning: when initialized here [-Wreorder]
5 | gtrModel::gtrModel(const Vdouble& freq,
| ^~~~~~~~
In file included from bestGtrModelParams.cpp:3:
bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)':
bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder]
175 | stochasticProcess& _sp;
| ^~~
bestGtrModelParams.h:173:34: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder]
173 | const gammaDistribution* _pProportionDist;
| ^~~~~~~~~~~~~~~~
bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder]
162 | C_evalGTRParamProportional( const GTRParam param,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp: In member function 'double gtrModel::get_a2c() const':
gtrModel.cpp:139:16: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
139 | return result;
| ^~~~~~
gtrModel.cpp:130:17: note: 'result' was declared here
130 | MDOUBLE result;
| ^~~~~~
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;
| ^~~~~~
gtrModel.cpp:144:17: note: 'result' was declared here
144 | MDOUBLE result;
| ^~~~~~
gtrModel.cpp: In member function 'double gtrModel::get_a2t() const':
gtrModel.cpp:167:16: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
167 | return result;
| ^~~~~~
gtrModel.cpp:158:17: note: 'result' was declared here
158 | MDOUBLE result;
| ^~~~~~
gtrModel.cpp: In member function 'double gtrModel::get_c2g() const':
gtrModel.cpp:181:16: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
181 | return result;
| ^~~~~~
gtrModel.cpp:172:17: note: 'result' was declared here
172 | MDOUBLE result;
| ^~~~~~
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;
| ^~~~~~
gtrModel.cpp:186:17: note: 'result' was declared here
186 | MDOUBLE result;
| ^~~~~~
gtrModel.cpp: In member function 'double gtrModel::get_g2t() const':
gtrModel.cpp:209:16: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized]
209 | return result;
| ^~~~~~
gtrModel.cpp:200:17: note: 'result' was declared here
200 | MDOUBLE result;
| ^~~~~~
ar rv libEvolTree.a AddLog.o NNiProp.o NNiSep.o Nni.o aaJC.o allTrees.o allTreesSeparateModel.o alphabet.o amino.o bestAlpha.o bestAlphaManyTrees.o bestHKYparam.o bootstrap.o bblEM.o bblEMfixRoot.o bblEMProprtional.o bblEMProportionalEB.o bblLSProportionalEB.o bblEMSeperate.o chebyshevAccelerator.o clustalFormat.o codon.o codonJC.o computeCounts.o computeDownAlg.o computeMarginalAlg.o computePijComponent.o computeUpAlg.o computeUpAlgFactors.o computeSubstitutionCounts.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o ConversionUtils.o countTableComponent.o datMatrixHolder.o distanceTable.o distribution.o errorMsg.o evaluateCharacterFreq.o fastStartTree.o fastaFormat.o findRateOfGene.o fromCountTableComponentToDistance.o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistancePropEB.o fromQtoPt.o generalGammaDistributionFixedCategories.o gammaDistribution.o gammaUtilities.o generalGammaDistribution.o getRandomWeights.o goldmanYangModel.o granthamChemicalDistances.o hky.o simulateWithDependence.o KH_calculation.o likeDist.o likeDistfixRoot.o likeDistProp.o likeDistPropEB.o likelihoodComputation.o likelihoodComputationFactors.o logFile.o maseFormat.o molphyFormat.o nexusFormat.o nj.o njConstrain.o nucJC.o nucleotide.o numRec.o Parameters.o phylipFormat.o pijAccelerator.o readDatMatrix.o readTree.o recognizeFormat.o replacementModel.o searchStatus.o seqContainerTreeMap.o sequence.o sequenceContainer.o simulateTree.o siteSpecificRate.o someUtil.o split.o splitMap.o splitTreeUtil.o stochasticProcess.o suffStatComponent.o talRandom.o tree.o treeIt.o treeUtil.o uniDistribution.o uniformDistribution.o cmdline2EvolObjs.o generalGammaDistributionLaguerre.o gammaDistributionLaguerre.o GLaguer.o givenRatesMLDistance.o distanceBasedSeqs2Tree.o posteriorDistance.o pairwiseGammaDistance.o doubleRep.o logRep.o indel.o indelModel.o mulAlphabet.o replacementModelSSRV.o stochasticProcessSSRV.o bestAlphaAndNu.o C_evalParamUSSRV.o matrixUtils.o betaOmegaDistribution.o betaUtilities.o betaDistribution.o geneticCodeHolder.o samplingSequences.o bblEM2USSRV.o bestParamUSSRV.o likeDist2USSRV.o ussrvModel.o likelihoodComputation2USSRV.o fromCountTableComponentToDistance2USSRV.o normalDist.o tamura92.o bestTamura92param.o phylipSequentialFormat.o simulateCodonsJumps.o simulateJumpsAbstract.o ssrvDistanceSeqs2Tree.o multipleStochasticProcess.o distributionPlusInvariant.o extremeValDistribution.o gammaDistributionFixedCategories.o generalGammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.o distributionPlusCategory.o simulateJumps.o computeJumps.o seqeuncesFilter.o optGammaMixtureLS.o mixtureDistribution.o suffStatGammaMixture.o GamMixtureOptimizer.o optGammaMixtureEM.o gainLossAlphabet.o wYangModel.o codonUtils.o likelihoodComputation2Codon.o likeDist2Codon.o unObservableData.o likelihoodComputationGL.o threeStateModel.o threeStateAlphabet.o oneTwoMoreModel.o betaDistributionFixedCategories.o betaDistributionFixedCategoriesWithOmegaUniform.o bblEM2codon.o bestAlphaAndK.o fromCountTableComponentToDistance2Codon.o gtrModel.o bestGtrModelParams.o simulateRateShiftJumps.o integerAlphabet.o
ar: creating libEvolTree.a
a - AddLog.o
a - NNiProp.o
a - NNiSep.o
a - Nni.o
a - aaJC.o
a - allTrees.o
a - allTreesSeparateModel.o
a - alphabet.o
a - amino.o
a - bestAlpha.o
a - bestAlphaManyTrees.o
a - bestHKYparam.o
a - bootstrap.o
a - bblEM.o
a - bblEMfixRoot.o
a - bblEMProprtional.o
a - bblEMProportionalEB.o
a - bblLSProportionalEB.o
a - bblEMSeperate.o
a - chebyshevAccelerator.o
a - clustalFormat.o
a - codon.o
a - codonJC.o
a - computeCounts.o
a - computeDownAlg.o
a - computeMarginalAlg.o
a - computePijComponent.o
a - computeUpAlg.o
a - computeUpAlgFactors.o
a - computeSubstitutionCounts.o
a - computePosteriorExpectationOfSubstitutions.o
a - computePosteriorExpectationOfSubstitutions_nonReversibleSp.o
a - ConversionUtils.o
a - countTableComponent.o
a - datMatrixHolder.o
a - distanceTable.o
a - distribution.o
a - errorMsg.o
a - evaluateCharacterFreq.o
a - fastStartTree.o
a - fastaFormat.o
a - findRateOfGene.o
a - fromCountTableComponentToDistance.o
a - fromCountTableComponentToDistancefixRoot.o
a - fromCountTableComponentToDistanceProp.o
a - fromCountTableComponentToDistancePropEB.o
a - fromQtoPt.o
a - generalGammaDistributionFixedCategories.o
a - gammaDistribution.o
a - gammaUtilities.o
a - generalGammaDistribution.o
a - getRandomWeights.o
a - goldmanYangModel.o
a - granthamChemicalDistances.o
a - hky.o
a - simulateWithDependence.o
a - KH_calculation.o
a - likeDist.o
a - likeDistfixRoot.o
a - likeDistProp.o
a - likeDistPropEB.o
a - likelihoodComputation.o
a - likelihoodComputationFactors.o
a - logFile.o
a - maseFormat.o
a - molphyFormat.o
a - nexusFormat.o
a - nj.o
a - njConstrain.o
a - nucJC.o
a - nucleotide.o
a - numRec.o
a - Parameters.o
a - phylipFormat.o
a - pijAccelerator.o
a - readDatMatrix.o
a - readTree.o
a - recognizeFormat.o
a - replacementModel.o
a - searchStatus.o
a - seqContainerTreeMap.o
a - sequence.o
a - sequenceContainer.o
a - simulateTree.o
a - siteSpecificRate.o
a - someUtil.o
a - split.o
a - splitMap.o
a - splitTreeUtil.o
a - stochasticProcess.o
a - suffStatComponent.o
a - talRandom.o
a - tree.o
a - treeIt.o
a - treeUtil.o
a - uniDistribution.o
a - uniformDistribution.o
a - cmdline2EvolObjs.o
a - generalGammaDistributionLaguerre.o
a - gammaDistributionLaguerre.o
a - GLaguer.o
a - givenRatesMLDistance.o
a - distanceBasedSeqs2Tree.o
a - posteriorDistance.o
a - pairwiseGammaDistance.o
a - doubleRep.o
a - logRep.o
a - indel.o
a - indelModel.o
a - mulAlphabet.o
a - replacementModelSSRV.o
a - stochasticProcessSSRV.o
a - bestAlphaAndNu.o
a - C_evalParamUSSRV.o
a - matrixUtils.o
a - betaOmegaDistribution.o
a - betaUtilities.o
a - betaDistribution.o
a - geneticCodeHolder.o
a - samplingSequences.o
a - bblEM2USSRV.o
a - bestParamUSSRV.o
a - likeDist2USSRV.o
a - ussrvModel.o
a - likelihoodComputation2USSRV.o
a - fromCountTableComponentToDistance2USSRV.o
a - normalDist.o
a - tamura92.o
a - bestTamura92param.o
a - phylipSequentialFormat.o
a - simulateCodonsJumps.o
a - simulateJumpsAbstract.o
a - ssrvDistanceSeqs2Tree.o
a - multipleStochasticProcess.o
a - distributionPlusInvariant.o
a - extremeValDistribution.o
a - gammaDistributionFixedCategories.o
a - generalGammaDistributionPlusInvariant.o
a - gammaDistributionPlusInvariant.o
a - distributionPlusCategory.o
a - simulateJumps.o
a - computeJumps.o
a - seqeuncesFilter.o
a - optGammaMixtureLS.o
a - mixtureDistribution.o
a - suffStatGammaMixture.o
a - GamMixtureOptimizer.o
a - optGammaMixtureEM.o
a - gainLossAlphabet.o
a - wYangModel.o
a - codonUtils.o
a - likelihoodComputation2Codon.o
a - likeDist2Codon.o
a - unObservableData.o
a - likelihoodComputationGL.o
a - threeStateModel.o
a - threeStateAlphabet.o
a - oneTwoMoreModel.o
a - betaDistributionFixedCategories.o
a - betaDistributionFixedCategoriesWithOmegaUniform.o
a - bblEM2codon.o
a - bestAlphaAndK.o
a - fromCountTableComponentToDistance2Codon.o
a - gtrModel.o
a - bestGtrModelParams.o
a - simulateRateShiftJumps.o
a - integerAlphabet.o
ranlib libEvolTree.a
make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny'
make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/libs'
cd programs;make all
make[2]: Entering directory '/build/reproducible-path/fastml-3.11/programs'
cd fastml && make all
cd gainLoss && make all
cd indelCoder && make all
make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml'
make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss'
make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder'
making depend
making depend
making depend
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp
character.cpp: In member function 'int character::getLongestGapStIndex()':
character.cpp:28:16: warning: 'longestGapStIndex' may be used uninitialized [-Wmaybe-uninitialized]
28 | return longestGapStIndex;
| ^~~~~~~~~~~~~~~~~
character.cpp:17:13: note: 'longestGapStIndex' was declared here
17 | int longestGapStIndex;
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp
indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()':
indelCoder.cpp:422:13: warning: unused variable 'gapNum' [-Wunused-variable]
422 | int gapNum = 1;
| ^~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp
indelCoder.cpp: In member function 'void indelCoder::printIndelSummary()':
indelCoder.cpp:587:14: warning: unused variable 'isSIC' [-Wunused-variable]
587 | bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC;
| ^~~~~
indelCoder.cpp:597:13: warning: unused variable 'seqLeng' [-Wunused-variable]
597 | int seqLeng = _sc.seqLen();
| ^~~~~~~
character.cpp: In member function 'void character::checkForTriangleInequality(int, int)':
character.cpp:6:70: warning: 'longestGapStIndex' may be used uninitialized [-Wmaybe-uninitialized]
6 | if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][longestGapStIndex]){
| ^
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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp
In file included from 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,
| ^~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bb_options.o bb_options.cpp
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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp
In file included from bbAlg.h:8,
from fastml.cpp:254:
bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)':
bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder]
14 | const string& _reportFileName;
| ^~~~~~~~~~~~~~~
bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder]
13 | const int _minNumOfNodesToVisit;
| ^~~~~~~~~~~~~~~~~~~~~
bbReport.h:10:18: warning: when initialized here [-Wreorder]
10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit)
| ^~~~~~~~~~~~~~~~~
In file included from bbAlg.h:8,
from bbAlg.cpp:1:
bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)':
bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder]
14 | const string& _reportFileName;
| ^~~~~~~~~~~~~~~
bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder]
13 | const int _minNumOfNodesToVisit;
| ^~~~~~~~~~~~~~~~~~~~~
bbReport.h:10:18: warning: when initialized here [-Wreorder]
10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit)
| ^~~~~~~~~~~~~~~~~
bbAlg.h: In constructor 'bbAlg::bbAlg(const tree&, std::vector<stochasticProcess>&, const sequenceContainer&, boundMethod, const std::string&, double, const distribution*)':
bbAlg.h:61:23: warning: 'bbAlg::_reportFileName' will be initialized after [-Wreorder]
61 | const string& _reportFileName;
| ^~~~~~~~~~~~~~~
bbAlg.h:60:27: warning: 'BandBReportAllPos bbAlg::BandBReportAllPos1' [-Wreorder]
60 | BandBReportAllPos BandBReportAllPos1; // report for all positions.
| ^~~~~~~~~~~~~~~~~~
bbAlg.cpp:7:1: warning: when initialized here [-Wreorder]
7 | bbAlg::bbAlg(const tree& et,
| ^~~~~
bbAlg.h:60:27: warning: 'bbAlg::BandBReportAllPos1' will be initialized after [-Wreorder]
60 | BandBReportAllPos BandBReportAllPos1; // report for all positions.
| ^~~~~~~~~~~~~~~~~~
bbAlg.h:29:21: warning: 'const tree& bbAlg::_et' [-Wreorder]
29 | const tree& _et;
| ^~~
bbAlg.cpp:7:1: warning: when initialized here [-Wreorder]
7 | bbAlg::bbAlg(const tree& et,
| ^~~~~
In file included from bbEvaluateSpecificAV.h:4:
bb_options.h: At global scope:
bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function]
62 | static const string usege_splash_screen() {
| ^~~~~~~~~~~~~~~~~~~
In file included from mainbb.h:4,
from fastml.cpp:1:
bb_options.h: At global scope:
bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function]
62 | static const string usege_splash_screen() {
| ^~~~~~~~~~~~~~~~~~~
In file included from bbNodeOrderAlg.h:5,
from bbAlg.h:5:
bb_options.h: At global scope:
bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function]
62 | static const string usege_splash_screen() {
| ^~~~~~~~~~~~~~~~~~~
In file included from bb_options.cpp:2:
bb_options.h: In constructor 'bb_options::bb_options(int&, char**)':
bb_options.h:49:16: warning: 'bb_options::reportFile' will be initialized after [-Wreorder]
49 | string reportFile;
| ^~~~~~~~~~
bb_options.h:44:16: warning: 'std::string bb_options::outFile_seq_joint' [-Wreorder]
44 | string outFile_seq_joint;
| ^~~~~~~~~~~~~~~~~
bb_options.cpp:6:1: warning: when initialized here [-Wreorder]
6 | bb_options::bb_options(int& argc, char *argv[]):
| ^~~~~~~~~~
bb_options.h:45:16: warning: 'bb_options::outFile_seq_marginal' will be initialized after [-Wreorder]
45 | string outFile_seq_marginal;
| ^~~~~~~~~~~~~~~~~~~~
bb_options.h:42:16: warning: 'std::string bb_options::outFile_prob_joint' [-Wreorder]
42 | string outFile_prob_joint;
| ^~~~~~~~~~~~~~~~~~
bb_options.cpp:6:1: warning: when initialized here [-Wreorder]
6 | bb_options::bb_options(int& argc, char *argv[]):
| ^~~~~~~~~~
bb_options.h:43:16: warning: 'bb_options::outFile_prob_marginal' will be initialized after [-Wreorder]
43 | string outFile_prob_marginal;
| ^~~~~~~~~~~~~~~~~~~~~
bb_options.h:24:16: warning: 'std::string bb_options::seqfile' [-Wreorder]
24 | string seqfile;
| ^~~~~~~
bb_options.cpp:6:1: warning: when initialized here [-Wreorder]
6 | bb_options::bb_options(int& argc, char *argv[]):
| ^~~~~~~~~~
bb_options.h:30:28: warning: 'bb_options::distributionName' will be initialized after [-Wreorder]
30 | distributionsNames distributionName;
| ^~~~~~~~~~~~~~~~
bb_options.h:26:23: warning: 'bb_options::SeqFileFormat bb_options::seqOutputFormat' [-Wreorder]
26 | SeqFileFormat seqOutputFormat;
| ^~~~~~~~~~~~~~~
bb_options.cpp:6:1: warning: when initialized here [-Wreorder]
6 | bb_options::bb_options(int& argc, char *argv[]):
| ^~~~~~~~~~
bb_options.h:41:16: warning: 'bb_options::outTreeFileAncestor' will be initialized after [-Wreorder]
41 | string outTreeFileAncestor;
| ^~~~~~~~~~~~~~~~~~~
bb_options.h:32:22: warning: 'bb_options::boundMethods bb_options::boundMethod' [-Wreorder]
32 | boundMethods boundMethod;
| ^~~~~~~~~~~
bb_options.cpp:6:1: warning: when initialized here [-Wreorder]
6 | bb_options::bb_options(int& argc, char *argv[]):
| ^~~~~~~~~~
bb_options.h:47:17: warning: 'bb_options::gammaPar' will be initialized after [-Wreorder]
47 | MDOUBLE gammaPar;
| ^~~~~~~~
bb_options.h:28:14: warning: 'bool bb_options::userProvideAlpha' [-Wreorder]
28 | bool userProvideAlpha;
| ^~~~~~~~~~~~~~~~
bb_options.cpp:6:1: warning: when initialized here [-Wreorder]
6 | bb_options::bb_options(int& argc, char *argv[]):
| ^~~~~~~~~~
bb_options.h:48:13: warning: 'bb_options::gammaCategies' will be initialized after [-Wreorder]
48 | int gammaCategies;
| ^~~~~~~~~~~~~
bb_options.h:36:26: warning: 'bb_options::modelNameOptions bb_options::modelName' [-Wreorder]
36 | modelNameOptions modelName;
| ^~~~~~~~~
bb_options.cpp:6:1: warning: when initialized here [-Wreorder]
6 | bb_options::bb_options(int& argc, char *argv[]):
| ^~~~~~~~~~
bb_options.h:39:14: warning: 'bb_options::useChebyshev' will be initialized after [-Wreorder]
39 | bool useChebyshev;
| ^~~~~~~~~~~~
bb_options.h:27:16: warning: 'std::string bb_options::treeOutFile' [-Wreorder]
27 | string treeOutFile;
| ^~~~~~~~~~~
bb_options.cpp:6:1: warning: when initialized here [-Wreorder]
6 | bb_options::bb_options(int& argc, char *argv[]):
| ^~~~~~~~~~
In file included from bbNodeOrderAlg.cpp:1:
bbNodeOrderAlg.h: In constructor 'bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)':
bbNodeOrderAlg.h:33:34: warning: 'bbNodeOrderAlg::_sc' will be initialized after [-Wreorder]
33 | const sequenceContainer& _sc;
| ^~~
bbNodeOrderAlg.h:32:30: warning: 'const computePijGam& bbNodeOrderAlg::_cpij' [-Wreorder]
32 | const computePijGam& _cpij;
| ^~~~~
bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder]
8 | bbNodeOrderAlg::bbNodeOrderAlg(const tree& et,
| ^~~~~~~~~~~~~~
In file included from bbfindBestAVDynProg.h:5,
from bbfindBestAVDynProg.cpp:1:
bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function]
62 | static const string usege_splash_screen() {
| ^~~~~~~~~~~~~~~~~~~
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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp
In file included from bbReport.cpp:1:
bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)':
bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder]
14 | const string& _reportFileName;
| ^~~~~~~~~~~~~~~
bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder]
13 | const int _minNumOfNodesToVisit;
| ^~~~~~~~~~~~~~~~~~~~~
bbReport.h:10:18: warning: when initialized here [-Wreorder]
10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit)
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp
In file included from 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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp
bbReport.h: In constructor 'BandBReport::BandBReport(const std::string&, int, int)':
bbReport.h:53:23: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder]
53 | const string& _reportFileName;
| ^~~~~~~~~~~~~~~
bbReport.h:51:19: warning: 'const int BandBReport::_position' [-Wreorder]
51 | const int _position;
| ^~~~~~~~~
bbReport.cpp:10:1: warning: when initialized here [-Wreorder]
10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) :
| ^~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp
computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)':
computeMarginalReconstruction.cpp:67:25: warning: unused variable 'likelihoodOfPos' [-Wunused-variable]
67 | MDOUBLE likelihoodOfPos = 0;
| ^~~~~~~~~~~~~~~
computeMarginalReconstruction.cpp:45:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable]
45 | MDOUBLE totalLikelihoodOfReconstruction = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
jointNoGamma.cpp: In member function 'void jointNoGamma::compute()':
jointNoGamma.cpp:23:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable]
23 | MDOUBLE totalLikelihoodOfReconstruction = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
jointNoGamma.cpp: In member function 'std::vector<int> jointNoGamma::computeJointAncestralFromSSC(int, const suffStatGlobalHomPos&, const suffStatGlobalHomPosJointNoGamma&, doubleRep&)':
jointNoGamma.cpp:108:33: warning: unused variable 'maxL' [-Wunused-variable]
108 | MDOUBLE maxL = VERYSMALL;
| ^~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp
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)
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp
In file included from 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,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp
In file included from gainLoss.h:35,
from gainLoss.cpp:20:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gainLossUtils.cpp:19:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
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 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() {
| ^~~~~~~~~~~~~~~~~~~
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<std::vector<stochasticProcess*> >&, 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<std::vector<stochasticProcess*> >&, distribution*, distribution*)':
gainLossUtils.cpp:788:17: warning: unused variable 'scale' [-Wunused-variable]
788 | MDOUBLE scale;
| ^~~~~
In file included from gainLoss.cpp:41:
bblLS.h: At global scope:
bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null]
50 | MDOUBLE curL =NULL);
| ^~~~
bblLS.h:58:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null]
58 | MDOUBLE curL =NULL);
| ^~~~
bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector<std::vector<stochasticProcess*> >&, const distribution*, const distribution*, Vdouble*, unObservableData*)':
bblLS.h:119:27: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder]
119 | unObservableData* _unObservableData_p;
| ^~~~~~~~~~~~~~~~~~~
bblLS.h:118:18: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder]
118 | Vdouble* _weights;
| ^~~~~~~~
bblLS.h:96:18: warning: when initialized here [-Wreorder]
96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector<vector<stochasticProcess*> >& spVVec,
| ^~~~~~~~~~~~~~
bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector<std::vector<stochasticProcess*> >&, const distribution*, const distribution*, Vdouble*, unObservableData*)':
bblLS.h:174:27: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder]
174 | unObservableData* _unObservableData_p;
| ^~~~~~~~~~~~~~~~~~~
bblLS.h:173:18: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder]
173 | Vdouble* _weights;
| ^~~~~~~~
bblLS.h:152:18: warning: when initialized here [-Wreorder]
152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector<vector<stochasticProcess*> >& spVVec,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLoss.h: In constructor 'gainLoss::gainLoss()':
gainLoss.h:266:28: warning: 'gainLoss::_unObservableData_p' will be initialized after [-Wreorder]
266 | unObservableData* _unObservableData_p;
| ^~~~~~~~~~~~~~~~~~~
gainLoss.h:240:23: warning: 'distribution* gainLoss::_lossDist' [-Wreorder]
240 | distribution* _lossDist;
| ^~~~~~~~~
gainLoss.cpp:63:1: warning: when initialized here [-Wreorder]
63 | gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL)
| ^~~~~~~~
gainLoss.h:240:23: warning: 'gainLoss::_lossDist' will be initialized after [-Wreorder]
240 | distribution* _lossDist;
| ^~~~~~~~~
gainLoss.h:239:23: warning: 'distribution* gainLoss::_gainDist' [-Wreorder]
239 | distribution* _gainDist;
| ^~~~~~~~~
gainLoss.cpp:63:1: warning: when initialized here [-Wreorder]
63 | gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL)
| ^~~~~~~~
gainLoss.h:273:19: warning: 'gainLoss::_refSeq' will be initialized after [-Wreorder]
273 | sequence* _refSeq; // the reference sequence
| ^~~~~~~
gainLoss.h:267:18: warning: 'Vdouble* gainLoss::_weightsUniqPatterns' [-Wreorder]
267 | Vdouble* _weightsUniqPatterns;
| ^~~~~~~~~~~~~~~~~~~~
gainLoss.cpp:63:1: warning: when initialized here [-Wreorder]
63 | gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL)
| ^~~~~~~~
In file included from optimizeGainLossModel.h:27,
from optimizeGainLossModel.cpp:17:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gainLoss.cpp: In member function 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)':
gainLoss.cpp:604:14: warning: unused variable 'missigDataChar' [-Wunused-variable]
604 | char missigDataChar = -2;
| ^~~~~~~~~~~~~~
optimizeGainLossModel.h: In constructor 'optimizeGainLossModel::optimizeGainLossModel(const tree&, stochasticProcess&, const sequenceContainer&, bool, double, int, Vdouble*, unObservableData*)':
optimizeGainLossModel.h:87:18: warning: 'optimizeGainLossModel::_weightsUniqPatterns' will be initialized after [-Wreorder]
87 | Vdouble* _weightsUniqPatterns;
| ^~~~~~~~~~~~~~~~~~~~
optimizeGainLossModel.h:86:27: warning: 'unObservableData* optimizeGainLossModel::_unObservableData_p' [-Wreorder]
86 | unObservableData* _unObservableData_p;
| ^~~~~~~~~~~~~~~~~~~
optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder]
20 | optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc,
| ^~~~~~~~~~~~~~~~~~~~~
optimizeGainLossModel.cpp:85:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable]
85 | MDOUBLE sumPijQij;
| ^~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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::startEvolTreeTopology(std::ostream&)':
gainLoss.cpp:1245:64: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){
| ^~
gainLoss.cpp:1245:45: note: add parentheses around left hand side expression to silence this warning
1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){
| ^~~~~~~~~~~~~~~~~~~
| ( )
indelCoder.cpp: In member function 'void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)':
indelCoder.cpp:175:33: warning: 'condition' may be used uninitialized [-Wmaybe-uninitialized]
175 | while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
indelCoder.cpp:170:22: note: 'condition' was declared here
170 | bool condition;
| ^~~~~~~~~
gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)':
gainLoss.cpp:1868:25: warning: unused variable 'sumPijQij' [-Wunused-variable]
1868 | MDOUBLE sumPijQij = normalizeQ(sp);
| ^~~~~~~~~
gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector<std::vector<stochasticProcess*> >&, distribution*, distribution*, unObservableData*, std::ostream&)':
gainLoss.cpp:1990:25: warning: unused variable 'sumPijQij' [-Wunused-variable]
1990 | MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist);
| ^~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp
In file included from optimizeGainLossModelVV.h:27,
from optimizeGainLossModelVV.cpp:17:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
optimizeGainLossModelVV.h: In constructor 'optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector<std::vector<stochasticProcess*> >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)':
optimizeGainLossModelVV.h:82:18: warning: 'optimizeGainLossModelVV::_weightsUniqPatterns' will be initialized after [-Wreorder]
82 | Vdouble* _weightsUniqPatterns;
| ^~~~~~~~~~~~~~~~~~~~
optimizeGainLossModelVV.h:81:27: warning: 'unObservableData* optimizeGainLossModelVV::_unObservableData_p' [-Wreorder]
81 | unObservableData* _unObservableData_p;
| ^~~~~~~~~~~~~~~~~~~
optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder]
25 | optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr,
| ^~~~~~~~~~~~~~~~~~~~~~~
optimizeGainLossModelVV.cpp:258:41: warning: unused variable 'currentlogL' [-Wunused-variable]
258 | MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p);
| ^~~~~~~~~~~
optimizeGainLossModelVV.cpp:76:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable]
76 | MDOUBLE sumPijQij;
| ^~~~~~~~~
gainLoss.cpp: In member function 'double gainLoss::computeDistanceFromRootForRecent(tree&)':
gainLoss.cpp:4205:14: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable]
4205 | bool isRecentBiggerAncient = true;
| ^~~~~~~~~~~~~~~~~~~~~
gainLoss.cpp: In member function 'double gainLoss::computeDistanceNearestOTUforRecent(tree&)':
gainLoss.cpp:4283:14: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable]
4283 | bool isRecentBiggerAncient = true;
| ^~~~~~~~~~~~~~~~~~~~~
gainLoss.cpp: In member function 'void gainLoss::multipleAllBranchesByFactorAtStart(double)':
gainLoss.cpp:4382:40: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){
| ^
gainLoss.cpp:4382:28: note: add parentheses around left hand side expression to silence this warning
4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){
| ^~~~~~~~~~~
| ( )
gainLoss.cpp: In member function 'void gainLoss::startSimultePosteriorExpectationOfChange(int, int)':
gainLoss.cpp:4951:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable]
4951 | MDOUBLE sumQii = 1.0;
| ^~~~~~
In file included from gainLossModel.cpp:17:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gainLossModel.h: In constructor 'gainLossModel::gainLossModel(double, Vdouble, bool, bool, bool, bool)':
gainLossModel.h:108:17: warning: 'gainLossModel::_gain' will be initialized after [-Wreorder]
108 | MDOUBLE _gain; // _Q[0][1]
| ^~~~~
gainLossModel.h:105:17: warning: 'Vdouble gainLossModel::_freq' [-Wreorder]
105 | Vdouble _freq;
| ^~~~~
gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder]
24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q):
| ^~~~~~~~~~~~~
gainLossModel.h:112:14: warning: 'gainLossModel::_isRootFreqEQstationary' will be initialized after [-Wreorder]
112 | bool _isRootFreqEQstationary;
| ^~~~~~~~~~~~~~~~~~~~~~~
gainLossModel.h:111:14: warning: 'bool gainLossModel::_isReversible' [-Wreorder]
111 | bool _isReversible;
| ^~~~~~~~~~~~~
gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder]
24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q):
| ^~~~~~~~~~~~~
gainLossModel.h:114:14: warning: 'gainLossModel::_isHGT_with_Q' will be initialized after [-Wreorder]
114 | bool _isHGT_with_Q;
| ^~~~~~~~~~~~~
gainLossModel.h:110:15: warning: 'q2pt* gainLossModel::_q2pt' [-Wreorder]
110 | q2pt *_q2pt; // dont use q2p
| ^~~~~
gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder]
24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q):
| ^~~~~~~~~~~~~
gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const std::string&)':
gainLossOptions.cpp:2111:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized]
2111 | return returnType;
| ^~~~~~~~~~
gainLossOptions.cpp:2098:24: note: 'returnType' was declared here
2098 | costMatrixType returnType;
| ^~~~~~~~~~
In file included from siteSpecificGL.cpp:24:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp
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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.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
ranlib libindelCoder.a
In file included from computePosteriorExpectationOfChange.cpp:25:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp
In file included from gainLoss.h:35,
from gainLossProject.cpp:17:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const std::string&)':
gainLossOptions.cpp:2064:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized]
2064 | return returnType;
| ^~~~~~~~~~
gainLossOptions.cpp:2047:27: note: 'returnType' was declared here
2047 | optimizationLevel returnType;
| ^~~~~~~~~~
gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const std::string&)':
gainLossOptions.cpp:2419:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized]
2419 | return returnType;
| ^~~~~~~~~~
gainLossOptions.cpp:2396:24: note: 'returnType' was declared here
2396 | simulationType returnType;
| ^~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp
In file included from /usr/include/c++/14/iostream:41,
from ../../libs/phylogeny/readTree.h:6,
from ../../libs/phylogeny/tree.h:7,
from ../../libs/phylogeny/simulateJumpsAbstract.h:5,
from ../../libs/phylogeny/simulateJumps.h:4,
from computePosteriorExpectationOfChange.h:24,
from computePosteriorExpectationOfChange.cpp:17:
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3:
/usr/include/c++/14/ostream:232:25: warning: 'Down' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)':
computePosteriorExpectationOfChange.cpp:215:27: note: 'Down' was declared here
215 | doubleRep resDXY, Down, Up;
| ^~~~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3:
/usr/include/c++/14/ostream:232:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)':
computePosteriorExpectationOfChange.cpp:215:33: note: 'Up' was declared here
215 | doubleRep resDXY, Down, Up;
| ^~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3:
/usr/include/c++/14/ostream:232:25: warning: 'pij' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)':
computePosteriorExpectationOfChange.cpp:216:17: note: 'pij' was declared here
216 | MDOUBLE pij;
| ^~~
In file included from gainLoss.h:35,
from rate4siteGL.h:24,
from rate4siteGL.cpp:17:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
rate4siteGL.h: In constructor 'rate4siteGL::rate4siteGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, unObservableData*)':
rate4siteGL.h:59:14: warning: 'rate4siteGL::_tr' will be initialized after [-Wreorder]
59 | tree _tr;
| ^~~
rate4siteGL.h:58:28: warning: 'stochasticProcess* rate4siteGL::_sp' [-Wreorder]
58 | stochasticProcess *_sp;
| ^~~
rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder]
24 | rate4siteGL::rate4siteGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, unObservableData* unObservableData_p):
| ^~~~~~~~~~~
rate4siteGL.cpp: In member function 'void rate4siteGL::printRatesBayes(std::ostream&, const Vdouble&)':
rate4siteGL.cpp:151:13: warning: unused variable 'precisionHigh' [-Wunused-variable]
151 | int precisionHigh = 5;
| ^~~~~~~~~~~~~
rate4siteGL.cpp:152:13: warning: unused variable 'precisionLow' [-Wunused-variable]
152 | int precisionLow = 3;
| ^~~~~~~~~~~~
In file included from gainLoss.h:35,
from gainLossOptimizer.h:24,
from gainLossOptimizer.cpp:17:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gainLoss.h:35,
from computeCountsGL.h:24,
from computeCountsGL.cpp:17:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
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;
| ^~
In file included from gainLossOptimizer.cpp:20:
bblLS.h: At global scope:
bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null]
50 | MDOUBLE curL =NULL);
| ^~~~
bblLS.h:58:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null]
58 | MDOUBLE curL =NULL);
| ^~~~
bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector<std::vector<stochasticProcess*> >&, const distribution*, const distribution*, Vdouble*, unObservableData*)':
bblLS.h:119:27: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder]
119 | unObservableData* _unObservableData_p;
| ^~~~~~~~~~~~~~~~~~~
bblLS.h:118:18: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder]
118 | Vdouble* _weights;
| ^~~~~~~~
bblLS.h:96:18: warning: when initialized here [-Wreorder]
96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector<vector<stochasticProcess*> >& spVVec,
| ^~~~~~~~~~~~~~
bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector<std::vector<stochasticProcess*> >&, const distribution*, const distribution*, Vdouble*, unObservableData*)':
bblLS.h:174:27: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder]
174 | unObservableData* _unObservableData_p;
| ^~~~~~~~~~~~~~~~~~~
bblLS.h:173:18: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder]
173 | Vdouble* _weights;
| ^~~~~~~~
bblLS.h:152:18: warning: when initialized here [-Wreorder]
152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector<vector<stochasticProcess*> >& spVVec,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, stochasticProcess*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)':
gainLossOptimizer.h:134:14: warning: 'gainLossOptimizer::_tr' will be initialized after [-Wreorder]
134 | tree _tr;
| ^~~
gainLossOptimizer.h:109:28: warning: 'stochasticProcess* gainLossOptimizer::_sp' [-Wreorder]
109 | stochasticProcess *_sp;
| ^~~
gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder]
25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc,
| ^~~~~~~~~~~~~~~~~
gainLossOptimizer.h:135:27: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder]
135 | sequenceContainer _sc;
| ^~~
gainLossOptimizer.h:93:17: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder]
93 | MDOUBLE _epsilonOptimization;
| ^~~~~~~~~~~~~~~~~~~~
gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder]
25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc,
| ^~~~~~~~~~~~~~~~~
gainLossOptimizer.h:104:18: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder]
104 | Vdouble* _weightsUniqPatterns;
| ^~~~~~~~~~~~~~~~~~~~
gainLossOptimizer.h:102:28: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder]
102 | unObservableData* _unObservableData_p;
| ^~~~~~~~~~~~~~~~~~~
gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder]
25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc,
| ^~~~~~~~~~~~~~~~~
gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, std::vector<std::vector<stochasticProcess*> >&, distribution*, distribution*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)':
gainLossOptimizer.h:139:23: warning: 'gainLossOptimizer::_lossDist' will be initialized after [-Wreorder]
139 | distribution* _lossDist;
| ^~~~~~~~~
gainLossOptimizer.h:135:27: warning: 'sequenceContainer gainLossOptimizer::_sc' [-Wreorder]
135 | sequenceContainer _sc;
| ^~~
gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder]
50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector<vector<stochasticProcess*> >& spVVec, distribution * gainDist, distribution * lossDist,
| ^~~~~~~~~~~~~~~~~
gainLossOptimizer.h:135:27: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder]
135 | sequenceContainer _sc;
| ^~~
gainLossOptimizer.h:93:17: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder]
93 | MDOUBLE _epsilonOptimization;
| ^~~~~~~~~~~~~~~~~~~~
gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder]
50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector<vector<stochasticProcess*> >& spVVec, distribution * gainDist, distribution * lossDist,
| ^~~~~~~~~~~~~~~~~
gainLossOptimizer.h:104:18: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder]
104 | Vdouble* _weightsUniqPatterns;
| ^~~~~~~~~~~~~~~~~~~~
gainLossOptimizer.h:102:28: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder]
102 | unObservableData* _unObservableData_p;
| ^~~~~~~~~~~~~~~~~~~
gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder]
50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector<vector<stochasticProcess*> >& spVVec, distribution * gainDist, distribution * lossDist,
| ^~~~~~~~~~~~~~~~~
computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, VVdouble&, double, bool)':
computeCountsGL.h:104:14: warning: 'computeCountsGL::_tr' will be initialized after [-Wreorder]
104 | tree _tr;
| ^~~
computeCountsGL.h:102:28: warning: 'stochasticProcess* computeCountsGL::_sp' [-Wreorder]
102 | stochasticProcess *_sp;
| ^~~
computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder]
28 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, VVdouble& logLpostPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent):
| ^~~~~~~~~~~~~~~
computeCountsGL.h:117:17: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder]
117 | MDOUBLE _distanceFromNearestOTUForRecent;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
computeCountsGL.h:113:14: warning: 'bool computeCountsGL::_isSilent' [-Wreorder]
113 | bool _isSilent;
| ^~~~~~~~~
computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder]
28 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, VVdouble& logLpostPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent):
| ^~~~~~~~~~~~~~~
computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, std::vector<std::vector<stochasticProcess*> >&, distribution*, distribution*, std::string&, VVVdouble&, double, bool)':
computeCountsGL.h:109:23: warning: 'computeCountsGL::_lossDist' will be initialized after [-Wreorder]
109 | distribution* _lossDist;
| ^~~~~~~~~
computeCountsGL.h:105:27: warning: 'sequenceContainer computeCountsGL::_sc' [-Wreorder]
105 | sequenceContainer _sc;
| ^~~
computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder]
33 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector<vector<stochasticProcess*> >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent):
| ^~~~~~~~~~~~~~~
computeCountsGL.h:117:17: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder]
117 | MDOUBLE _distanceFromNearestOTUForRecent;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
computeCountsGL.h:113:14: warning: 'bool computeCountsGL::_isSilent' [-Wreorder]
113 | bool _isSilent;
| ^~~~~~~~~
computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder]
33 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector<vector<stochasticProcess*> >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent):
| ^~~~~~~~~~~~~~~
gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengths(int)':
gainLossOptimizer.cpp:498:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable]
498 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLossOptimizer.cpp:543:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable]
543 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLossOptimizer.cpp:487:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable]
487 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengthsvv(int)':
gainLossOptimizer.cpp:634:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable]
634 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLossOptimizer.cpp:677:33: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable]
677 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLossOptimizer.cpp:623:17: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable]
623 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gainLoss.h:35,
from computeCorrelations.h:25,
from computeCorrelations.cpp:17:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
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
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp
ranlib libfastml.a
computeCorrelations.cpp: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)':
computeCorrelations.cpp:130:13: warning: unused variable 'numOfbranches' [-Wunused-variable]
130 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node
| ^~~~~~~~~~~~~
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;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml
computeCorrelations.cpp:348:21: warning: unused variable 'typeIndex' [-Wunused-variable]
348 | int typeIndex = corIndex % _EventTypes.size(); // in case both Spearman and pearson are used
| ^~~~~~~~~
computeCorrelations.cpp: In member function 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)':
computeCorrelations.cpp:559:30: warning: NULL used in arithmetic [-Wpointer-arith]
559 | if(!simCorrelStream==NULL)
| ^~~~
computeCorrelations.cpp:569:38: warning: NULL used in arithmetic [-Wpointer-arith]
569 | if(!simCorrelStream==NULL)
| ^~~~
computeCorrelations.cpp:579:38: warning: NULL used in arithmetic [-Wpointer-arith]
579 | if(!simCorrelStream==NULL)
| ^~~~
computeCorrelations.cpp:584:30: warning: NULL used in arithmetic [-Wpointer-arith]
584 | if(!simCorrelStream==NULL)
| ^~~~
computeCorrelations.cpp: In member function 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector<std::vector<bool> >&, VVVVdouble&, VVVdouble&, std::map<int, std::map<int, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)':
computeCorrelations.cpp:676:37: warning: variable 'prevNumberOfSimulationsInRange' set but not used [-Wunused-but-set-variable]
676 | int prevNumberOfSimulationsInRange = 1;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
computeCorrelations.cpp:677:37: warning: variable 'prevNumberOfSimulationPointsMoreExtremeOrEqToCorr' set but not used [-Wunused-but-set-variable]
677 | int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
computeCorrelations.cpp:679:37: warning: unused variable 'numOfBinsWithLowerSignificance' [-Wunused-variable]
679 | int numOfBinsWithLowerSignificance = 0; // allow 2 "bin-iteration" even with lower significance to mitigate chance of "missing" higher significance in lower bin
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
computeCorrelations.cpp:680:38: warning: unused variable 'isNextLowerBinAllowed' [-Wunused-variable]
680 | bool isNextLowerBinAllowed = true;
| ^~~~~~~~~~~~~~~~~~~~~
computeCorrelations.cpp: In member function 'void computeCorrelations::produceSymeticMatrix(VVVdouble&, bool)':
computeCorrelations.cpp:894:26: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses]
894 | if(!numOfSites_A == numOfSites_B){
| ^~
computeCorrelations.cpp:894:12: note: add parentheses around left hand side expression to silence this warning
894 | if(!numOfSites_A == numOfSites_B){
| ^~~~~~~~~~~~~
| ( )
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp
computeCorrelations.cpp: In member function 'void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::string*)':
computeCorrelations.cpp:1009:14: warning: unused variable 'isPearson' [-Wunused-variable]
1009 | bool isPearson = false;
| ^~~~~~~~~
computeCorrelations.cpp:1025:13: warning: unused variable 'numOfbranches' [-Wunused-variable]
1025 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node
| ^~~~~~~~~~~~~
computeCorrelations.cpp: In member function 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map<int, std::map<int, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> > > >&, std::vector<std::vector<bool> >&, Vdouble&, Vint&, Vint&)':
computeCorrelations.cpp:1347:67: warning: narrowing conversion of 'gainLossOptions::_pValueCutOffForBootStrap' from 'double' to 'float' [-Wnarrowing]
1347 | float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001};
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
computeCorrelations.cpp:1300:14: warning: variable 'it_siteB' set but not used [-Wunused-but-set-variable]
1300 | it_B it_siteB = it_siteA->second.begin();
| ^~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp
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 -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp
In file included from gainLoss.h:35,
from gainLoss4site.h:24,
from gainLoss4site.cpp:17:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector<std::vector<stochasticProcess*> >, 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<std::vector<stochasticProcess*> > gainLoss4site::_spVVec' [-Wreorder]
61 | vector<vector<stochasticProcess*> > _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 gainLoss.h:35,
from simulateOnePos.cpp:32:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bblLS.cpp:17:
bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null]
50 | MDOUBLE curL =NULL);
| ^~~~
bblLS.h:58:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null]
58 | MDOUBLE curL =NULL);
| ^~~~
In file included from gainLoss.h:35,
from simulateChangesAlongTree.cpp:20:
gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)':
gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder]
186 | MDOUBLE _loss; // _Q[1][0]
| ^~~~~
gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder]
128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)
| ^
gainLossModel.h:127:18: warning: when initialized here [-Wreorder]
127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector<std::vector<stochasticProcess*> >&, const distribution*, const distribution*, Vdouble*, unObservableData*)':
bblLS.h:119:27: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder]
119 | unObservableData* _unObservableData_p;
| ^~~~~~~~~~~~~~~~~~~
bblLS.h:118:18: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder]
118 | Vdouble* _weights;
| ^~~~~~~~
bblLS.h:96:18: warning: when initialized here [-Wreorder]
96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector<vector<stochasticProcess*> >& spVVec,
| ^~~~~~~~~~~~~~
bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector<std::vector<stochasticProcess*> >&, const distribution*, const distribution*, Vdouble*, unObservableData*)':
bblLS.h:174:27: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder]
174 | unObservableData* _unObservableData_p;
| ^~~~~~~~~~~~~~~~~~~
bblLS.h:173:18: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder]
173 | Vdouble* _weights;
| ^~~~~~~~
bblLS.h:152:18: warning: when initialized here [-Wreorder]
152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector<vector<stochasticProcess*> >& spVVec,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, stochasticProcess*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)':
bblLS.cpp:36:21: warning: NULL used in arithmetic [-Wpointer-arith]
36 | if (curL == NULL)
| ^~~~
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
| ^~~~~~~~~~~~~~
bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, std::vector<std::vector<stochasticProcess*> >&, const distribution*, const distribution*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)':
bblLS.cpp:112:21: warning: NULL used in arithmetic [-Wpointer-arith]
112 | if (curL == NULL)
| ^~~~
simulateOnePos.cpp: In member function 'void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::string)':
simulateOnePos.cpp:181:30: warning: unused variable 'isRevers' [-Wunused-variable]
181 | bool isRevers = false;
| ^~~~~~~~
simulateOnePos.cpp:202:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable]
202 | MDOUBLE sumQii = 1.0;
| ^~~~~~
In file included from sankoffReconstructGL.cpp:17:
sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)':
sankoffReconstructGL.h:85:16: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder]
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 '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:
gainLossModel.h:173:28: warning: 'currM2' may be used uninitialized [-Wmaybe-uninitialized]
173 | _Q[1][1] = -_loss;
| ^~~~~~
gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)':
gainLoss.cpp:1842:17: note: 'currM2' was declared here
1842 | MDOUBLE currM2;
| ^~~~~~
gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector<std::vector<stochasticProcess*> >&, distribution*, distribution*, unObservableData*, std::ostream&)':
gainLoss.cpp:1974:39: warning: 'currGainBeta' may be used uninitialized [-Wmaybe-uninitialized]
1974 | updateGainBeta(currGainBeta,spVVec,gainDist,lossDist);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLoss.cpp:1940:17: note: 'currGainBeta' was declared here
1940 | MDOUBLE currGainBeta;
| ^~~~~~~~~~~~
gainLoss.cpp:1978:40: warning: 'currLossAlpha' may be used uninitialized [-Wmaybe-uninitialized]
1978 | updateLossAlpha(currLossAlpha,spVVec,gainDist,lossDist);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLoss.cpp:1942:17: note: 'currLossAlpha' was declared here
1942 | MDOUBLE currLossAlpha; // Loss (for non-reversible model only)
| ^~~~~~~~~~~~~
gainLoss.cpp:1980:47: warning: 'currLossBeta' may be used uninitialized [-Wmaybe-uninitialized]
1980 | updateLossBeta(currLossBeta,spVVec,gainDist,lossDist);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLoss.cpp:1943:17: note: 'currLossBeta' was declared here
1943 | MDOUBLE currLossBeta;
| ^~~~~~~~~~~~
gainLoss.cpp:1982:56: warning: 'currLossProbInvariant' may be used uninitialized [-Wmaybe-uninitialized]
1982 | updateLossProbInvariant(currLossProbInvariant,lossDist);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLoss.cpp:1944:17: note: 'currLossProbInvariant' was declared here
1944 | MDOUBLE currLossProbInvariant;
| ^~~~~~~~~~~~~~~~~~~~~
gainLoss.cpp:2031:50: warning: 'bestGainProbInvariant' may be used uninitialized [-Wmaybe-uninitialized]
2031 | if(probInvariant) updateGainProbInvariant(bestGainProbInvariant,gainDist);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLoss.cpp:1930:17: note: 'bestGainProbInvariant' was declared here
1930 | MDOUBLE bestGainProbInvariant = 0.5;
| ^~~~~~~~~~~~~~~~~~~~~
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/iostream:41,
from ../../libs/phylogeny/readTree.h:6,
from ../../libs/phylogeny/tree.h:7,
from ../../libs/phylogeny/simulateJumpsAbstract.h:5,
from ../../libs/phylogeny/simulateJumps.h:4,
from computePosteriorExpectationOfChange.h:24,
from gainLoss.cpp:19:
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3896:33:
/usr/include/c++/14/ostream:232:25: warning: 'AlphaRate' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)':
gainLoss.cpp:3852:17: note: 'AlphaRate' was declared here
3852 | MDOUBLE AlphaRate,Gain,Loss,Theta;
| ^~~~~~~~~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3896:62:
/usr/include/c++/14/ostream:232:25: warning: 'Loss' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)':
gainLoss.cpp:3852:32: note: 'Loss' was declared here
3852 | MDOUBLE AlphaRate,Gain,Loss,Theta;
| ^~~~
In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits<char>]',
inlined from 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3896:74:
/usr/include/c++/14/ostream:232:25: warning: 'Theta' may be used uninitialized [-Wmaybe-uninitialized]
232 | { return _M_insert(__f); }
| ~~~~~~~~~^~~~~
gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)':
gainLoss.cpp:3852:37: note: 'Theta' was declared here
3852 | MDOUBLE AlphaRate,Gain,Loss,Theta;
| ^~~~~
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;
| ^~~~~~~~~
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;
| ^~~~~~~~
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<freqOfHighCorrPrev && Nmin_lower < medianNminOfRealData){
| ^~
computeCorrelations.cpp:406:25: note: 'expextedFreq' was declared here
406 | MDOUBLE expextedFreq;
| ^~~~~~~~~~~~
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;
| ^~~~~~~~
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;
| ^~~~~~~~
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 libgainLoss.a gainLossOptions.o gainLoss.o gainLossUtils.o optimizeGainLossModel.o optimizeGainLossModelVV.o ../../libs/phylogeny/likelihoodComputationGL.o gainLossModel.o siteSpecificGL.o computePosteriorExpectationOfChange.o gainLossProject.o gainLossOptimizer.o ancestralReconstructStates.o rate4siteGL.o computeCountsGL.o computeCorrelations.o gainLoss4site.o simulateChangesAlongTree.o simulateOnePos.o bblLS.o sankoffReconstructGL.o
ar: creating libgainLoss.a
a - gainLossOptions.o
a - gainLoss.o
a - gainLossUtils.o
a - optimizeGainLossModel.o
a - optimizeGainLossModelVV.o
a - ../../libs/phylogeny/likelihoodComputationGL.o
a - gainLossModel.o
a - siteSpecificGL.o
a - computePosteriorExpectationOfChange.o
a - gainLossProject.o
a - gainLossOptimizer.o
a - ancestralReconstructStates.o
a - rate4siteGL.o
a - computeCountsGL.o
a - computeCorrelations.o
a - gainLoss4site.o
a - simulateChangesAlongTree.o
a - simulateOnePos.o
a - bblLS.o
a - sankoffReconstructGL.o
ranlib libgainLoss.a
g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libgainLoss.a ../../libs/phylogeny/libEvolTree.a -o gainLoss
make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss'
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 -j11 test
make[1]: Entering directory '/build/reproducible-path/fastml-3.11'
cd libs;make test
cd programs;make test
make[2]: Entering directory '/build/reproducible-path/fastml-3.11/libs'
cd phylogeny && make test
make[2]: Entering directory '/build/reproducible-path/fastml-3.11/programs'
cd fastml && make test
cd gainLoss && make test
cd indelCoder && make 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/indelCoder'
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/programs/gainLoss'
if [ -d tests ] ; then cd tests && make -k ; fi
make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss'
make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/programs'
make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny'
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 -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. split_test.cpp ../libEvolTree.a -lEvolTree -o split_test
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -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 -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 -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 -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. checkTreeLikelihoodGivenBranches.cpp ../libEvolTree.a -lEvolTree -o checkTreeLikelihoodGivenBranches
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistBetweenThemGamma.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistBetweenThemGamma
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistanceK2P.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistanceK2P
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. doubleRep.cpp ../libEvolTree.a -lEvolTree -o doubleRep
g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. readTreeWithComments.cpp ../libEvolTree.a -lEvolTree -o readTreeWithComments
./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp
diff readTreeWithComments.out.tmp readTreeWithComments.out.standard
./split_test > split_test.out.tmp
diff split_test.out.tmp split_test.out.standard
./doubleRep > doubleRep.out.tmp
diff doubleRep.out.tmp doubleRep.out.standard
./splitMap_test > splitMap_test.out.tmp
diff splitMap_test.out.tmp splitMap_test.out.standard
./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp
diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard
./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp
diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard
./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp
diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard
./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp
diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard
./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp
diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard
make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny/tests'
make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny'
make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/libs'
echo test
test
make[1]: Leaving directory '/build/reproducible-path/fastml-3.11'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/fastml/
make -j11 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'
cd phylogeny && make all
make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny'
make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/libs'
cd programs;make install
make[2]: Entering directory '/build/reproducible-path/fastml-3.11/programs'
cd fastml && make install
cd gainLoss && make install
cd indelCoder && make install
make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder'
mkdir -p ../../bin
make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml'
mkdir -p ../../bin
cp indelCoder ../../bin/indelCoder
cp fastml ../../bin/fastml
make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss'
mkdir -p ../../bin
cp gainLoss ../../bin/gainLoss
make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder'
make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml'
make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss'
make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/programs'
make[1]: Leaving directory '/build/reproducible-path/fastml-3.11'
dh_install
dh_installdocs
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'fastml' in '../fastml_3.11-4_i386.deb'.
dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.11-4_i386.deb'.
dpkg-genbuildinfo --build=binary -O../fastml_3.11-4_i386.buildinfo
dpkg-genchanges --build=binary -O../fastml_3.11-4_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
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/18634 and its subdirectories
I: Current time: Tue Feb 25 18:29:25 -12 2025
I: pbuilder-time-stamp: 1740551365