Mon Apr 22 21:06:57 UTC 2024 I: starting to build fastml/trixie/armhf on jenkins on '2024-04-22 21:06' Mon Apr 22 21:06:57 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_17/3562/console.log Mon Apr 22 21:06:57 UTC 2024 I: Downloading source for trixie/fastml=3.11-4 --2024-04-22 21:06:57-- http://deb.debian.org/debian/pool/main/f/fastml/fastml_3.11-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1900 (1.9K) [text/prs.lines.tag] Saving to: ‘fastml_3.11-4.dsc’ 0K . 100% 303M=0s 2024-04-22 21:06:57 (303 MB/s) - ‘fastml_3.11-4.dsc’ saved [1900/1900] Mon Apr 22 21:06:57 UTC 2024 I: fastml_3.11-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: fastml Binary: fastml Architecture: any Version: 3.11-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://fastml.tau.ac.il/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/fastml Vcs-Git: https://salsa.debian.org/med-team/fastml.git Build-Depends: debhelper-compat (= 13) Package-List: fastml deb science optional arch=any Checksums-Sha1: 2bc5d72d636c37c0890c36b7e426d24131bfac8d 849058 fastml_3.11.orig.tar.gz 7530d47e861350740cb869801c1ac13b844ada7f 10164 fastml_3.11-4.debian.tar.xz Checksums-Sha256: 2d1ec87116eae1163177631ad39083db01cdd78ffb8d119bebbdbb6a43e99451 849058 fastml_3.11.orig.tar.gz 31206f832cf5500066e5e5dfd448b224c2a410bf265e3961ea2ddb84a37fc191 10164 fastml_3.11-4.debian.tar.xz Files: 4443e346151ff347816dcba7e700212d 849058 fastml_3.11.orig.tar.gz c2d36bf402afb8462c79bfbead23547e 10164 fastml_3.11-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWxO1cRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFxTQ/+P6vte5yk0+ZDdWEcoa3cZlVp57GH26N1 siM2zI/ZaDPJRP9wOxtbpBPv335pctuRbeWDO1j6iVVd/RuK0nz4Cnys5yQVX4bw 8f6lpXQ85DncnepGSG8o5849lFSDP0/oP0pJAL23RzIcFFKICYnGRBSdbvuFlcKh lk1hfntISLhQJy/Mb/Yxr5avQxTqrR5V34yDn9e2jb7ozp5C4Iov5Opwac1ZdAdW lURcm+5VqEDnrCF5mqpJMSgS9ikIPBhLQqFVDt3UkiEZyJk5VQ8PWr3LRw/HVC0z 3nEyEG1rLSw1hLJeN96qLfl2R9VGsT4Eg9J+7xBvzuK6YeDNRahgKmE4GGBrGShI dIhJdkTtssLsI7TX++Y4uNynMR1BDYHzgl0EkPMxoZA7JGUsyyX/lNXu96F9eqpY IqlUL04fuoj+7laVetWzZ8HIFPU7TYxMffiJORAv+0o/CI6DKzgDykByoNX+1LCP M/b4cEE2M1NxjweShL1zw25u451LsJZiFSWjYYJpqVb0M+7MXb6Lhv8DmK5dVD1m AbymUv1TkUumxNjrAOo5KVOC7ToPmHN+aPtTeCaBVIR4PpHvxFbe5QCsTROGIQGX 0eU8q+oZ4wwmWz5evixLgXUHqh8IuQsRRzGBA0/iVNBSN8ziB8ntImLkc4lWRN10 f+RrC7uPnwU= =SAiw -----END PGP SIGNATURE----- Mon Apr 22 21:06:57 UTC 2024 I: Checking whether the package is not for us Mon Apr 22 21:06:57 UTC 2024 I: Starting 1st build on remote node virt32b-armhf-rb.debian.net. Mon Apr 22 21:06:57 UTC 2024 I: Preparing to do remote build '1' on virt32b-armhf-rb.debian.net. Mon Apr 22 21:23:03 UTC 2024 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 22 09:07:09 -12 2024 I: pbuilder-time-stamp: 1713820029 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: 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 gpgv: Signature made Wed Jan 24 16:31:19 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./fastml_3.11-4.dsc: no acceptable signature found 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/28038/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='ab2b506162ca4b309ed4362ffb944606' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='28038' 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.3foiQUBY/pbuilderrc_fSN4 --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.3foiQUBY/b1 --logfile b1/build.log fastml_3.11-4.dsc' SUDO_GID='112' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32b 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 21 07:14 /bin -> usr/bin I: user script /srv/workspace/pbuilder/28038/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: armhf Maintainer: Debian Pbuilder Team 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 ... 19635 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} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{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 18.3 MB of archives. After unpacking 68.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Fetched 18.3 MB in 1s (25.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19635 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../02-libmagic1_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic1:armhf (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-2+b1_armhf.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-6_armhf.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../22-libelf1_0.190-1+b1_armhf.deb ... Unpacking libelf1:armhf (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1:armhf (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libelf1:armhf (0.190-1+b1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-15) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... 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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf 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 -j3 clean make[2]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make clean cd programs;make clean make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs' cd phylogeny && make clean make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs' cd fastml && make clean cd gainLoss && make clean make[4]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' cd indelCoder && make clean make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' 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/gainLoss' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/libs' 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/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 -j3 "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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o alphabet.o alphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o amino.o amino.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from allTrees.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void allTrees::recursiveFind(tree, const stochasticProcess&, const sequenceContainer&, std::vector, const Vdouble*, int, double)' at allTrees.cpp:99:32: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlpha.o bestAlpha.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)': bestAlpha.cpp:371:17: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] 371 | MDOUBLE oldA=0; | ^~~~ bestAlphaManyTrees.cpp: In function 'void bestAlpha::optimizeAlphaNG_EM_PROP_n_alpha(tree&, std::vector&, std::vector&, const std::vector*>*, std::vector&, double&, int, double)': bestAlphaManyTrees.cpp:184:17: warning: variable 'ax' set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ bestAlphaManyTrees.cpp:184:20: warning: variable 'bx' set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ bestAlphaManyTrees.cpp:184:23: warning: variable 'cx' set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from bestAlpha.h:6, from bestAlpha.cpp:6: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bestAlphasAndBBLProportional::bestAlphasAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double)' at bestAlpha.cpp:129:29: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from bestHKYparam.h:6, from bestHKYparam.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bestHkyParamAlphaAndBBLProportional::bestHkyParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)' at bestHKYparam.cpp:197:18: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from bblEM.h:5, from bblEMProportionalEB.cpp:2: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void bblEMProportionalEB::allocatePlacePropEB()' at bblEMProportionalEB.cpp:106:31: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o clustalFormat.o clustalFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeCounts.o computeCounts.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeDownAlg.o computeDownAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeMarginalAlg.o computeMarginalAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlg.o computeUpAlg.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from codon.h:6, from codon.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void codonUtility::readCodonUsage(const std::string&, Vdouble&, const codon&)' at codon.cpp:460:19: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void codonUtility::getCodonUsage(const sequenceContainer&, Vint&, Vdouble&)' at codon.cpp:436:19: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static double codonUtility::calcCodonAdaptationIndex(const sequenceContainer&, const Vdouble&, Vdouble&)' at codon.cpp:517:17: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp In file included from 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): | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from computeUpAlgFactors.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeUpAlg::fillComputeUpSpecificGlobalRateFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double, std::vector&)' at computeUpAlgFactors.cpp:128:16: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&, std::vector&)' at computeUpAlgFactors.cpp:42:16: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, std::vector&)' at computeUpAlgFactors.cpp:84:16: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp In file included from /usr/include/c++/13/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]', inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3: /usr/include/c++/13/ostream:223:25: warning: 'Down' may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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]', inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3: /usr/include/c++/13/ostream:223:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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]', inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3: /usr/include/c++/13/ostream:223:25: warning: 'pij' may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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; | ^~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from computeSubstitutionCounts.h:4: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3, inlined from 'virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)' at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:39:108: /usr/include/c++/13/ostream:223:25: warning: 'Down' may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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]', 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++/13/ostream:223:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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]', 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++/13/ostream:223:25: warning: 'pij' may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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 -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeSubstitutionCounts::run()' at computeSubstitutionCounts.cpp:38:62: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeSubstitutionCounts::run()' at computeSubstitutionCounts.cpp:39:63: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:225:48: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:356:43: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)' at computeSubstitutionCounts.cpp:357:42: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from distanceTable.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void giveDistanceTable(const distanceMethod*, const sequenceContainer&, VVdouble&, std::vector >&, const std::vector*)' at distanceTable.cpp:12:55: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from fastStartTree.cpp:15: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'std::vector eliminateHalf(std::vector&, sequenceContainer&, stochasticProcess&, std::ostream&, int)' at fastStartTree.cpp:36:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'std::vector eliminateHalf(std::vector&, sequenceContainer&, stochasticProcess&, std::ostream&, int)' at fastStartTree.cpp:36:6: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'std::vector eliminateHalf(std::vector&, sequenceContainer&, stochasticProcess&, std::ostream&, int)' at fastStartTree.cpp:36:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp In file included from fromCountTableComponentToDistancePropEB.cpp:3: fromCountTableComponentToDistancePropEB.h: In constructor 'fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB(const std::vector >&, int, multipleStochasticProcess*, const gammaDistribution*, double, double)': fromCountTableComponentToDistancePropEB.h:29:19: warning: 'fromCountTableComponentToDistancePropEB::_nodeID' will be initialized after [-Wreorder] 29 | const int _nodeID; | ^~~~~~~ fromCountTableComponentToDistancePropEB.h:28:34: warning: 'const gammaDistribution* fromCountTableComponentToDistancePropEB::_pProportionDist' [-Wreorder] 28 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] 6 | fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from generalGammaDistributionFixedCategories.h:9, from generalGammaDistributionFixedCategories.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void generalGammaDistributionFixedCategories::setDefaultBoundaries(int)' at generalGammaDistributionFixedCategories.cpp:131:17: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void generalGammaDistributionFixedCategories::fill_mean()' at generalGammaDistributionFixedCategories.cpp:72:15: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void generalGammaDistributionFixedCategories::setDefaultBoundaries(int)' at generalGammaDistributionFixedCategories.cpp:131:17, inlined from 'generalGammaDistributionFixedCategories::generalGammaDistributionFixedCategories(double, double, int)' at generalGammaDistributionFixedCategories.cpp:33:22: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from fromQtoPt.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void generalGammaDistributionFixedCategories::setDefaultBoundaries(int)' at generalGammaDistributionFixedCategories.cpp:131:17, inlined from 'virtual void generalGammaDistributionFixedCategories::change_number_of_categories(int)' at generalGammaDistributionFixedCategories.cpp:43:22: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'VVdouble get1PamFromCountMatrix(const std::vector&, const VVdouble&)' at fromQtoPt.cpp:256:17: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from generalGammaDistribution.h:11, from generalGammaDistribution.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void generalGammaDistribution::setGammaParameters(int, double, double)' at generalGammaDistribution.cpp:70:19, inlined from 'generalGammaDistribution::generalGammaDistribution(double, double, int)' at generalGammaDistribution.cpp:34:20: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void generalGammaDistribution::setGammaParameters(int, double, double)' at generalGammaDistribution.cpp:70:19: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void generalGammaDistribution::setGammaParameters(int, double, double)' at generalGammaDistribution.cpp:70:19, inlined from 'virtual void generalGammaDistribution::change_number_of_categories(int)' at generalGammaDistribution.cpp:52:20: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void generalGammaDistribution::setGammaParameters(int, double, double)' at generalGammaDistribution.cpp:70:19, inlined from 'virtual void generalGammaDistribution::setAlpha(double)' at generalGammaDistribution.cpp:40:20, inlined from 'virtual void generalGammaDistribution::setAlpha(double)' at generalGammaDistribution.cpp:37:6: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void generalGammaDistribution::setGammaParameters(int, double, double)' at generalGammaDistribution.cpp:70:19, inlined from 'virtual void generalGammaDistribution::setBeta(double)' at generalGammaDistribution.cpp:46:20, inlined from 'virtual void generalGammaDistribution::setBeta(double)' at generalGammaDistribution.cpp:43:6: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)': goldmanYangModel.cpp:8:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] 8 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV): | ^~~~~~~~~~~~~~~~ goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, const Vdouble&, bool)': goldmanYangModel.cpp:18:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] 18 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): | ^~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from goldmanYangModel.h:6, from goldmanYangModel.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void goldmanYangModel::homogenousFreq()' at goldmanYangModel.h:30:76, inlined from 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)' at goldmanYangModel.cpp:10:17: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)' at goldmanYangModel.cpp:12:48: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'goldmanYangModel::goldmanYangModel(double, double, codon&, const Vdouble&, bool)' at goldmanYangModel.cpp:21:48: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp In file included from generalGammaDistributionPlusInvariant.h:9, from simulateWithDependence.h:35, from simulateWithDependence.cpp:1: distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.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 likeDist.cpp:210:13: warning: variable 'oldIntervalSize' set but not used [-Wunused-but-set-variable] 210 | MDOUBLE oldIntervalSize = currentIntervalSize; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from tree.h:6, from simulateWithDependence.h:29: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'double sim_with_dep::simulate_with_dependence(std::string, double, double, int, int, double, int, double, double, int)' at simulateWithDependence.cpp:65:19: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'double sim_with_dep::simulate_with_dependence(std::string, double, double, int, int, double, int, double, double, int)' at simulateWithDependence.cpp:66:19: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'double sim_with_dep::simulate_with_dependence(std::string, double, double, int, int, double, int, double, double, int)' at simulateWithDependence.cpp:67:19: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'double sim_with_dep::simulate_with_dependence(std::string, double, double, int, int, double, int, double, double, int)' at simulateWithDependence.cpp:68:19: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp likelihoodComputation.cpp: In function 'double likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(const tree&, const sequenceContainer&, const stochasticProcess&, const Vdouble*, unObservableData*)': likelihoodComputation.cpp:43:45: warning: 'LforMissingData' may be used uninitialized [-Wmaybe-uninitialized] 43 | LofPos = LofPos / (1- LforMissingData); | ~~^~~~~~~~~~~~~~~~~~ likelihoodComputation.cpp:27:17: note: 'LforMissingData' was declared here 27 | MDOUBLE LforMissingData; | ^~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o molphyFormat.o molphyFormat.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from likelihoodComputation.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:394:22: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:397:30: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:402:16: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:138:26: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)' at likelihoodComputation.cpp:141:38: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:380:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'double likelihoodComputation::getTreeLikelihoodFromUpSpecifcRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalHom&, VdoubleRep&, const Vdouble*)' at likelihoodComputation.cpp:530:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VdoubleRep&, const Vdouble*, unObservableData*)' at likelihoodComputation.cpp:350:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp In file included from /usr/include/c++/13/cassert:44, from njConstrain.cpp:4: njConstrain.cpp: In function 'tree::TreeNode* joinNodesToSubtree(tree&, tree::TreeNode*&, tree::TreeNode*&)': njConstrain.cpp:92:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 92 | assert (k=fatherNode->getNumberOfSons()+2); // both s1 and s2 should have been skiped | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from nj.h:8, from nj.cpp:6: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void NJalg::UpdateDistanceTableAndCurrentNodes(std::vector&, VVdouble&, tree::nodeP, tree::nodeP, tree::nodeP, int, int)' at nj.cpp:265:66: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] 306 | //* for (i=1;i >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double performKSTest(const uniformDistribution&, Vdouble&)' at numRec.cpp:465:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double performKSTest(const uniformDistribution&, Vdouble&)' at numRec.cpp:465:6: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from numRec.h:13, from numRec.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void houseHolder(VVdouble&, VVdouble&)' at numRec.cpp:167:14: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void houseHolder(VVdouble&, VVdouble&)' at numRec.cpp:169:10: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void houseHolder(VVdouble&, VVdouble&)' at numRec.cpp:170:10: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void houseHolder(VVdouble&, VVdouble&)' at numRec.cpp:171:10: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readTree.o readTree.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o recognizeFormat.o recognizeFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModel.o replacementModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o searchStatus.o searchStatus.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequence.o sequence.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from readDatMatrix.h:6, from readDatMatrix.cpp:14: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'VVdouble fromWagSandFreqToQ(const VVdouble&, const Vdouble&)' at readDatMatrix.cpp:259:46: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:95:52, inlined from 'void pupAll::fillMatrices(const std::string&, const Vdouble&)' at readDatMatrix.cpp:159:25: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:96:13, inlined from 'void pupAll::fillMatrices(const std::string&, const Vdouble&)' at readDatMatrix.cpp:159:25: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readDatMatrixFromFile(const std::string&, VVdouble&, Vdouble&)' at readDatMatrix.cpp:52:52: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readDatMatrixFromFile(const std::string&, VVdouble&, Vdouble&)' at readDatMatrix.cpp:53:13: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:95:52: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void readDatMatrixFromString(const std::string&, VVdouble&, Vdouble&, int)' at readDatMatrix.cpp:96:13: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequenceContainer.o sequenceContainer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o siteSpecificRate.o siteSpecificRate.cpp sequenceContainer.cpp: In member function '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 > 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 -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o split.o split.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from someUtil.cpp:9: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = vecElem; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1854 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double computeFDRthreshold(Vdouble&, double, bool)' at someUtil.cpp:715:7: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double computeFDRthreshold(Vdouble&, double, bool)' at someUtil.cpp:715:7: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcess.o stochasticProcess.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1631:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1631 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1631:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1631:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In function 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1926:27: /usr/include/c++/13/bits/stl_algo.h:1910:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1910 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double orderVec(const std::vector&, std::vector&)' at someUtil.cpp:829:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void orderVec(const Vdouble&, std::vector >&)' at someUtil.cpp:896:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void orderRankNoTies(const std::vector&, std::vector&)' at someUtil.cpp:878:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double computeQuantileFrac(const std::vector&, double)' at someUtil.cpp:113:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double computeQuantileFrac(const std::vector&, double)' at someUtil.cpp:114:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double computeQuantile(const std::vector&, double)' at someUtil.cpp:132:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double computeQuantile(const std::vector&, double)' at someUtil.cpp:133:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double computeMedian(const std::vector&)' at someUtil.cpp:90:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double computeMedian(const std::vector&)' at someUtil.cpp:91:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void orderRankNoTies(const std::vector&, std::vector&)' at someUtil.cpp:878:6, inlined from 'double calcRankCorrelation2(const Vdouble&, const Vdouble&)' at someUtil.cpp:664:17: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp: In constructor 'tree::tree(const std::string&)': tree.cpp:180:11: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 180 | if (in.is_open()) | ^~ tree.cpp:182:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 182 | create_names_to_internal_nodes(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp treeUtil.cpp: In function 'std::vector getNexusTreesFromFile(const std::string&)': treeUtil.cpp:371:32: warning: variable 'itStrStart' set but not used [-Wunused-but-set-variable] 371 | string::const_iterator itStrStart = it->begin(); | ^~~~~~~~~~ treeUtil.cpp:372:32: warning: variable 'itStrEnd' set but not used [-Wunused-but-set-variable] 372 | string::const_iterator itStrEnd = it->end(); | ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from uniformDistribution.h:22, from uniformDistribution.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void uniformDistribution::setUniformParameters(int, double, double)' at uniformDistribution.cpp:35:19: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void uniformDistribution::setUniformParameters(int, double, double)' at uniformDistribution.cpp:35:19, inlined from 'uniformDistribution::uniformDistribution(int, double, double)' at uniformDistribution.cpp:9:22: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void uniformDistribution::setUniformParameters(int, double, double)' at uniformDistribution.cpp:35:19, inlined from 'virtual void uniformDistribution::change_number_of_categories(int)' at uniformDistribution.cpp:62:22, inlined from 'virtual void uniformDistribution::change_number_of_categories(int)' at uniformDistribution.cpp:58:6: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from generalGammaDistributionLaguerre.h:26, from generalGammaDistributionLaguerre.cpp:2: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'virtual void generalGammaDistributionLaguerre::fillRatesAndProbs(int)' at generalGammaDistributionLaguerre.cpp:87:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'virtual void generalGammaDistributionLaguerre::fillRatesAndProbs(int)' at generalGammaDistributionLaguerre.cpp:88:19: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'virtual void generalGammaDistributionLaguerre::setGammaParameters(int, double, double)' at generalGammaDistributionLaguerre.cpp:52:19: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'virtual void generalGammaDistributionLaguerre::setGammaParameters(int, double, double)' at generalGammaDistributionLaguerre.cpp:53:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'virtual void generalGammaDistributionLaguerre::setGammaParameters(int, double, double)' at generalGammaDistributionLaguerre.cpp:52:19, inlined from 'generalGammaDistributionLaguerre::generalGammaDistributionLaguerre(double, double, int)' at generalGammaDistributionLaguerre.cpp:25:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'virtual void generalGammaDistributionLaguerre::setGammaParameters(int, double, double)' at generalGammaDistributionLaguerre.cpp:53:23, inlined from 'generalGammaDistributionLaguerre::generalGammaDistributionLaguerre(double, double, int)' at generalGammaDistributionLaguerre.cpp:25:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from GLaguer.cpp:2: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void GLaguer::GetPhylipLaguer(int, double, Vdouble&, Vdouble&)' at GLaguer.cpp:76:15: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void GLaguer::GetPhylipLaguer(int, double, Vdouble&, Vdouble&)' at GLaguer.cpp:77:16: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void GLaguer::gaulag(Vdouble&, Vdouble&, double, int)' at GLaguer.cpp:27:10: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void GLaguer::gaulag(Vdouble&, Vdouble&, double, int)' at GLaguer.cpp:28:10: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp In file included from distanceBasedSeqs2Tree.cpp:12: bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': 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 -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp In file included from pairwiseGammaDistance.h:6, from pairwiseGammaDistance.cpp:3: likeDist.h:51:19: warning: 'virtual const double likeDist::giveDistance(const sequence&, const sequence&, const std::vector*, double*) const' was hidden [-Woverloaded-virtual=] 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*) const' 32 | const MDOUBLE giveDistance(const sequence& s1, | ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from replacementModel.h:6, from replacementModelSSRV.h:6, from replacementModelSSRV.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void replacementModelSSRV::updateQ()' at replacementModelSSRV.cpp:105:15: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from matrixUtils.h:4, from matrixUtils.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'Vdouble getSubDiagonalFromMatrix(VVdouble&)' at matrixUtils.cpp:20:21: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void appendVectors(VVdouble&, const VVdouble&)' at matrixUtils.cpp:175:21: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'Vdouble getDiagonalFromMatrix(VVdouble&)' at matrixUtils.cpp:13:21: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistribution.o betaDistribution.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void readDoubleVecFromFile(Vdouble&, std::string)' at matrixUtils.cpp:198:17: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void readMatrixFromFile(VVdouble&, std::string)' at matrixUtils.cpp:49:19: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 _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 -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from betaDistribution.h:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void betaDistribution::setBetaParameters(int, double, double)' at betaDistribution.cpp:86:19, inlined from 'betaDistribution::betaDistribution(double, double, int, discretizationType)' at betaDistribution.cpp:36:19: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void betaDistribution::setBetaParameters(int, double, double)' at betaDistribution.cpp:86:19: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void betaDistribution::setBetaParameters(int, double, double)' at betaDistribution.cpp:86:19, inlined from 'virtual void betaDistribution::change_number_of_categories(int)' at betaDistribution.cpp:68:19: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void betaDistribution::setBetaParameters(int, double, double)' at betaDistribution.cpp:86:19, inlined from 'virtual void betaDistribution::setAlpha(double)' at betaDistribution.cpp:48:19, inlined from 'virtual void betaDistribution::setAlpha(double)' at betaDistribution.cpp:45:6: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void betaDistribution::setBetaParameters(int, double, double)' at betaDistribution.cpp:86:19, inlined from 'virtual void betaDistribution::setBeta(double)' at betaDistribution.cpp:54:19, inlined from 'virtual void betaDistribution::setBeta(double)' at betaDistribution.cpp:51:6: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from likelihoodComputation2USSRV.h:5, from likelihoodComputation2USSRV.cpp:2: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'double likelihoodComputation2USSRV::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const sequenceContainer&, const ussrvModel&, const suffStatGlobalGam&, const suffStatGlobalHom&, VdoubleRep&, const Vdouble*)' at likelihoodComputation2USSRV.cpp:79:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from bestTamura92param.h:6, from bestTamura92param.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateCodonsJumps.h:4, from simulateCodonsJumps.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'virtual void simulateCodonsJumps::init()' at simulateCodonsJumps.cpp:62:37: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double, double)' at bestTamura92param.cpp:250:18: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o extremeValDistribution.o extremeValDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp In file included from gammaDistributionPlusInvariant.h:9, from gammaDistributionPlusInvariant.cpp:1: distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp In file included from generalGammaDistributionPlusInvariant.h:9, from generalGammaDistributionPlusInvariant.cpp:1: distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeJumps.o computeJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp 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 -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp In file included from seqeuncesFilter.h:6, from seqeuncesFilter.cpp:1: In member function 'const sequence& sequenceContainer::operator[](int) const', inlined from 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)' at seqeuncesFilter.cpp:175:16: sequenceContainer.h:31:88: warning: 'refID' may be used uninitialized [-Wmaybe-uninitialized] 31 | const sequence& operator[](const int id) const {return _seqDataVec[_id2place[id]];} | ^ seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)': seqeuncesFilter.cpp:165:13: note: 'refID' was declared here 165 | int refID; | ^~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateJumps.h:4, from simulateJumps.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void simulateJumps::init()' at simulateJumps.cpp:63:23: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp In file included from /usr/include/arm-linux-gnueabihf/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/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 >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from 'mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)' at mixtureDistribution.cpp:84:24: /usr/include/c++/13/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 file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]', inlined from 'mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)' at mixtureDistribution.cpp:84:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: warning: 'pComp' may be used uninitialized [-Wmaybe-uninitialized] 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72: /usr/include/c++/13/bits/vector.tcc: In constructor 'mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)': /usr/include/c++/13/bits/vector.tcc:445:7: note: by argument 3 of type 'generalGammaDistribution* const&' to 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*; _Alloc = std::allocator]' declared here 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:72:43: note: 'pComp' declared here 72 | 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 >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from 'mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)' at mixtureDistribution.cpp:52:24: /usr/include/c++/13/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 member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]', inlined from 'mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)' at mixtureDistribution.cpp:52:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: warning: 'pComp' may be used uninitialized [-Wmaybe-uninitialized] 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In constructor 'mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)': /usr/include/c++/13/bits/vector.tcc:445:7: note: by argument 3 of type 'generalGammaDistribution* const&' to 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*; _Alloc = std::allocator]' declared here 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:40:43: note: 'pComp' declared here 40 | generalGammaDistribution* pComp; | ^~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void mixtureDistribution::change_number_of_components(int)' at mixtureDistribution.cpp:190:30: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp suffStatGammaMixture.cpp: In member function 'void suffStatGammaMixture::computeStatistics()': suffStatGammaMixture.cpp:123:33: warning: variable 'Exp_Rk' set but not used [-Wunused-but-set-variable] 123 | MDOUBLE Exp_Rk, Exp_LogRk, sum; | ^~~~~~ suffStatGammaMixture.cpp: In member function 'double suffStatGammaMixture::computeQ()': suffStatGammaMixture.cpp:224:25: warning: unused variable 'first' [-Wunused-variable] 224 | MDOUBLE first = _MkVec[comp] * log(P_k); | ^~~~~ suffStatGammaMixture.cpp:225:25: warning: unused variable 'second' [-Wunused-variable] 225 | MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k); | ^~~~~~ suffStatGammaMixture.cpp:226:25: warning: unused variable 'third' [-Wunused-variable] 226 | MDOUBLE third = -_MkVec[comp] * gammln(alpha_k); | ^~~~~ suffStatGammaMixture.cpp:227:25: warning: unused variable 'fourth' [-Wunused-variable] 227 | MDOUBLE fourth = -_AkVec[comp]*beta_k; | ^~~~~~ suffStatGammaMixture.cpp:228:25: warning: unused variable 'fifth' [-Wunused-variable] 228 | MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0); | ^~~~~ suffStatGammaMixture.cpp:216:17: warning: variable 'res2' set but not used [-Wunused-but-set-variable] 216 | MDOUBLE res2 = 0.0; | ^~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp 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 /usr/include/c++/13/vector:72, from definitions.h:18, from suffStatGammaMixture.h:16, from suffStatGammaMixture.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatGammaMixture::allocatePlaceForSuffStat()' at suffStatGammaMixture.cpp:30:15: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatGammaMixture::allocatePlaceForSuffStat()' at suffStatGammaMixture.cpp:32:15: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void suffStatGammaMixture::allocatePlaceForSuffStat()' at suffStatGammaMixture.cpp:34:15: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from GamMixtureOptimizer.cpp:7: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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))); | ^~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double GamMixtureOptimizer::findBestParamManyStarts(Vint, Vint, std::vector, Vdouble, const Vdouble*, std::ofstream*)' at GamMixtureOptimizer.cpp:73:8: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double GamMixtureOptimizer::findBestParamManyStarts(Vint, Vint, std::vector, Vdouble, const Vdouble*, std::ofstream*)' at GamMixtureOptimizer.cpp:73:8: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double GamMixtureOptimizer::findBestParamManyStarts(Vint, Vint, std::vector, Vdouble, const Vdouble*, std::ofstream*)' at GamMixtureOptimizer.cpp:99:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double GamMixtureOptimizer::findBestParamManyStarts(Vint, Vint, std::vector, Vdouble, const Vdouble*, std::ofstream*)' at GamMixtureOptimizer.cpp:99:6: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double GamMixtureOptimizer::findBestParamManyStarts(Vint, Vint, std::vector, Vdouble, const Vdouble*, std::ofstream*)' at GamMixtureOptimizer.cpp:73:8: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from optGammaMixtureEM.cpp:7: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from optGammaMixtureEM.h:11: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mixtureDistribution&}; _Tp = mixtureDistribution; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {mixtureDistribution}; _Tp = mixtureDistribution; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mixtureDistribution; _Alloc = std::allocator]', inlined from 'double optGammaMixtureEM::findBestParamManyStarts(int, int, int, int, double, double, std::ofstream*)' at optGammaMixtureEM.cpp:51:21: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {mixtureDistribution}; _Tp = mixtureDistribution; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = mixtureDistribution; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'double optGammaMixtureEM::findBestParamManyStarts(int, int, int, int, double, double, std::ofstream*)' at optGammaMixtureEM.cpp:53:21: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double optGammaMixtureEM::findBestParamManyStarts(int, int, int, int, double, double, std::ofstream*)' at optGammaMixtureEM.cpp:64:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double optGammaMixtureEM::findBestParamManyStarts(int, int, int, int, double, double, std::ofstream*)' at optGammaMixtureEM.cpp:64:6: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double optGammaMixtureEM::findBestParamManyStarts(int, int, int, int, double, double, std::ofstream*)' at optGammaMixtureEM.cpp:64:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from replacementModel.h:6, from wYangModel.h:4, from wYangModel.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from codonUtils.cpp:3: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'wYangModel::wYangModel(double, double, bool, codon*)' at wYangModel.cpp:11:47: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'wYangModel::wYangModel(double, double, const Vdouble&, bool, codon*)' at wYangModel.cpp:20:47: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from nucleotide.h:7, from codonUtils.h:5, from codonUtils.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'Vdouble freqCodonF3x4(const sequenceContainer&, codon*)' at codonUtils.cpp:73:25: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from likelihoodComputation2Codon.h:6, from likelihoodComputation2Codon.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'double likelihoodComputation2Codon::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, Vdouble&, const distribution*, const Vdouble*)' at likelihoodComputation2Codon.cpp:90:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void kaks2Color(const Vdouble&, const Vdouble&, const sequence&, std::string, codon*)' at codonUtils.cpp:237:30: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void kaks2Color(const Vdouble&, const Vdouble&, const sequence&, std::string, codon*)' at codonUtils.cpp:238:27: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void kaks2Color(const Vdouble&, const Vdouble&, const sequence&, std::string, codon*)' at codonUtils.cpp:246:7: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void kaks2Color(const Vdouble&, const Vdouble&, const sequence&, std::string, codon*)' at codonUtils.cpp:246:7: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from likelihoodComputationGL.h:4, from likelihoodComputationGL.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'double likelihoodComputationGL::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const std::vector >&, const suffStatGlobalGam&, const distribution*, const distribution*, const Vdouble*, unObservableData*, Vdouble*)' at likelihoodComputationGL.cpp:146:22: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from betaDistributionFixedCategories.h:9, from betaDistributionFixedCategories.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void betaDistributionFixedCategories::setDefaultBoundaries(int)' at betaDistributionFixedCategories.cpp:132:18: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void betaDistributionFixedCategories::fill_mean()' at betaDistributionFixedCategories.cpp:79:15: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void betaDistributionFixedCategories::setDefaultBoundaries(int)' at betaDistributionFixedCategories.cpp:132:18, inlined from 'betaDistributionFixedCategories::betaDistributionFixedCategories()' at betaDistributionFixedCategories.cpp:42:22: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void betaDistributionFixedCategories::setDefaultBoundaries(int)' at betaDistributionFixedCategories.cpp:132:18, inlined from 'betaDistributionFixedCategories::betaDistributionFixedCategories(double, double, int)' at betaDistributionFixedCategories.cpp:34:22: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void betaDistributionFixedCategories::setDefaultBoundaries(int)' at betaDistributionFixedCategories.cpp:132:18, inlined from 'virtual void betaDistributionFixedCategories::change_number_of_categories(int)' at betaDistributionFixedCategories.cpp:50:22: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2codon.o bblEM2codon.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndK.o bestAlphaAndK.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gtrModel.o gtrModel.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestGtrModelParams.o bestGtrModelParams.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp 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; | ^~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from replacementModel.h:6, from gtrModel.h:4: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)' at gtrModel.cpp:15:50: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o integerAlphabet.o integerAlphabet.cpp In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from bestGtrModelParams.h:6: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateRateShiftJumps.h:4, from simulateRateShiftJumps.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bestGtrModelProportional::bestGtrModelProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)' at bestGtrModelParams.cpp:223:18: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'void simulateRateShiftJumps::init(std::vector)' at simulateRateShiftJumps.cpp:102:37: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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 make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' cd indelCoder && make all making depend making depend make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' making depend g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoder.o indelCoder.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': indelCoder.cpp:422:13: warning: unused variable 'gapNum' [-Wunused-variable] 422 | int gapNum = 1; | ^~~~~~ indelCoder.cpp: In member function 'void indelCoder::printIndelSummary()': indelCoder.cpp:587:14: warning: unused variable 'isSIC' [-Wunused-variable] 587 | bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; | ^~~~~ indelCoder.cpp:597:13: warning: unused variable 'seqLeng' [-Wunused-variable] 597 | int seqLeng = _sc.seqLen(); | ^~~~~~~ In file included from bbAlg.h:8, from fastml.cpp:254: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const std::string&, int)': bbReport.h:14:23: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:19: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp In file included from mainbb.h:4, from fastml.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp 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&, 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 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() { | ^~~~~~~~~~~~~~~~~~~ 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; | ^~~~~~~~~~ indelCoder.cpp: In member function 'void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)': indelCoder.cpp:175:33: warning: 'condition' may be used uninitialized [-Wmaybe-uninitialized] 175 | while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indelCoder.cpp:170:22: note: 'condition' was declared here 170 | bool condition; | ^~~~~~~~~ gainLossOptions.cpp: In static member function 'static gainLossOptions::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 /usr/include/c++/13/vector:72, from ../../libs/phylogeny/definitions.h:18, from ../../libs/phylogeny/computePijComponent.h:6, from bbAlg.h:4: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'double bbAlg::bbReconstructAllPositions(sequenceContainer&)' at bbAlg.cpp:88:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const std::string&)': gainLossOptions.cpp:2419:16: warning: 'returnType' may be used uninitialized [-Wmaybe-uninitialized] 2419 | return returnType; | ^~~~~~~~~~ gainLossOptions.cpp:2396:24: note: 'returnType' was declared here 2396 | simulationType returnType; | ^~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp In file included from bbEvaluateSpecificAV.cpp:1: bbEvaluateSpecificAV.h: In constructor 'bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&)': bbEvaluateSpecificAV.h:34:34: warning: 'bbEvaluateSpecificAV::_sc' will be initialized after [-Wreorder] 34 | const sequenceContainer& _sc; | ^~~ bbEvaluateSpecificAV.h:31:30: warning: 'const computePijGam& bbEvaluateSpecificAV::_bbcpij' [-Wreorder] 31 | const computePijGam& _bbcpij; | ^~~~~~~ bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] 3 | bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, | ^~~~~~~~~~~~~~~~~~~~ bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': bbEvaluateSpecificAV.cpp:65:33: warning: unused variable 'rate' [-Wunused-variable] 65 | MDOUBLE rate = _sp.rates(categor); // the r. | ^~~~ In file included from gainLoss.h:30, from gainLoss.cpp:20: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp In file included from bbEvaluateSpecificAV.h:4: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ ../../libs/phylogeny/distributionPlusInvariant.h: At global scope: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLoss.cpp:25: ../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.cpp:41: bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 58 | MDOUBLE curL =NULL); | ^~~~ bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:119:27: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:18: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:18: warning: when initialized here [-Wreorder] 96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~ bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:174:27: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:18: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:18: warning: when initialized here [-Wreorder] 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.h: In constructor 'gainLoss::gainLoss()': gainLoss.h:266:28: warning: 'gainLoss::_unObservableData_p' will be initialized after [-Wreorder] 266 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ 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) | ^~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)': gainLoss.cpp:604:14: warning: unused variable 'missigDataChar' [-Wunused-variable] 604 | char missigDataChar = -2; | ^~~~~~~~~~~~~~ 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()){ | ^~~~~~~~~~~~~~~~~~~ | ( ) gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': gainLoss.cpp:1868:25: warning: unused variable 'sumPijQij' [-Wunused-variable] 1868 | MDOUBLE sumPijQij = normalizeQ(sp); | ^~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': gainLoss.cpp:1990:25: warning: unused variable 'sumPijQij' [-Wunused-variable] 1990 | MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); | ^~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp 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; | ^~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o character.o character.cpp In file included from bbfindBestAVDynProg.h:5, from bbfindBestAVDynProg.cpp:1: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp 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; | ^~~~~~~~~~~~~~~~~ character.cpp: In member function 'void character::checkForTriangleInequality(int, int)': character.cpp:6:70: warning: 'longestGapStIndex' may be used uninitialized [-Wmaybe-uninitialized] 6 | if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][longestGapStIndex]){ | ^ character.cpp:17:13: note: 'longestGapStIndex' was declared here 17 | int longestGapStIndex; | ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp 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, | ^~~~~~~~~~~~~~ ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o ar: creating libindelCoder.a a - indelCoder.o a - indelCoderOptions.o a - indelCoderProject.o a - indelCoderUtils.o a - character.o a - gaps.o ranlib libindelCoder.a g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder 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() { | ^~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from bbNodeOrderAlg.cpp:5: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossUtils.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void bbNodeOrderAlg::putBack(tree::TreeNode*&, const doubleRep&)' at bbNodeOrderAlg.cpp:53:27: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from gainLossUtils.cpp:19: gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../../libs/phylogeny/distributionPlusInvariant.h: At global scope: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.cpp:20: ../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by 'gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)' 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ gainLossUtils.cpp: In function 'void printTreeWithValuesAsBP(std::ostream&, tree::TreeNode* const&, Vstring, VVVdouble*, bool)': gainLossUtils.cpp:72:19: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 72 | if(probs) | ^ gainLossUtils.cpp:88:27: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 88 | if(probs) | ^ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'void bbNodeOrderAlg::rankRemainingNodesAccordingToTheirMarginalProb(int)' at bbNodeOrderAlg.cpp:67:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void bbNodeOrderAlg::rankRemainingNodesAccordingToTheirMarginalProb(int)' at bbNodeOrderAlg.cpp:70:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void bbNodeOrderAlg::rankRemainingNodesAccordingToTheirMarginalProb(int)' at bbNodeOrderAlg.cpp:70:6: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ gainLossUtils.cpp: In function 'void updateGainBeta(double, std::vector >&, distribution*, distribution*, bool)': gainLossUtils.cpp:481:17: warning: variable 'normFactor' set but not used [-Wunused-but-set-variable] 481 | MDOUBLE normFactor; | ^~~~~~~~~~ gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': gainLossUtils.cpp:788:17: warning: unused variable 'scale' [-Wunused-variable] 788 | MDOUBLE scale; | ^~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'std::vector bbNodeOrderAlg::findBestOrderInNode(tree::nodeP, int) const' at bbNodeOrderAlg.cpp:123:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'std::vector bbNodeOrderAlg::findBestOrderInNode(tree::nodeP, int) const' at bbNodeOrderAlg.cpp:126:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'std::vector bbNodeOrderAlg::findBestOrderInNode(tree::nodeP, int) const' at bbNodeOrderAlg.cpp:126:6: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bb_options.o bb_options.cpp 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[]): | ^~~~~~~~~~ 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 'double getRateBeta(distribution*)': gainLossUtils.cpp:312:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] 312 | return res; | ^~~ gainLossUtils.cpp:285:17: note: 'res' was declared here 285 | MDOUBLE res; | ^~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp 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 >&, 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; | ^~~~~~~~~~~~~~~~~~~~~ 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) | ^~~~~~~~~~~~~~~~~ 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 ) : | ^~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../../libs/phylogeny/definitions.h:18, from bbReport.h:4: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void BandBReport::report(std::string, int, int, doubleRep, doubleRep, doubleRep, doubleRep)' at bbReport.cpp:32:23: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void BandBReport::report(std::string, int, int, doubleRep, doubleRep, doubleRep, doubleRep)' at bbReport.cpp:33:25: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void BandBReport::report(std::string, int, int, doubleRep, doubleRep, doubleRep, doubleRep)' at bbReport.cpp:34:23: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void BandBReport::report(std::string, int, int, doubleRep, doubleRep, doubleRep, doubleRep)' at bbReport.cpp:35:21: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.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; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/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]', inlined from 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3896:33: /usr/include/c++/13/ostream:223:25: warning: 'AlphaRate' may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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]', inlined from 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3896:62: /usr/include/c++/13/ostream:223:25: warning: 'Loss' may be used uninitialized [-Wmaybe-uninitialized] 223 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)': gainLoss.cpp:3852:32: note: 'Loss' was declared here 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; | ^~~~ In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)' at gainLoss.cpp:3896:74: /usr/include/c++/13/ostream:223:25: warning: 'Theta' may be used uninitialized [-Wmaybe-uninitialized] 223 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscape(stochasticProcess*)': gainLoss.cpp:3852:37: note: 'Theta' was declared here 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; | ^~~~~ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, from optimizeGainLossModel.h:27, from optimizeGainLossModel.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from computeMarginalReconstruction.cpp:8: /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 In file included from /usr/include/c++/13/bits/stl_algo.h:61: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Distance = int; _Tp = pair >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 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); | ~~~~~~~~~~^~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:3947:17: note: 'AlphaGain' was declared here 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; | ^~~~~~~~~ gainLoss.cpp:3980:73: warning: 'AlphaLoss' may be used uninitialized [-Wmaybe-uninitialized] 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); | ~~~~~~~~~~^~~~~~~~~~~ gainLoss.cpp:3947:27: note: 'AlphaLoss' was declared here 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; | ^~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../../libs/phylogeny/definitions.h:18, from computeMarginalReconstruction.h:4, from computeMarginalReconstruction.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair, std::allocator > >}; _Tp = std::pair >; _Alloc = std::allocator > >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector > >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair, std::allocator > >}; _Tp = std::pair >; _Alloc = std::allocator > >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair >; _Alloc = std::allocator > >]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void computeMarginalReconstruction::outputTheMarginalProbForEachCharForEachNodePos(std::ostream&, int)' at computeMarginalReconstruction.cpp:175:18: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >*, vector > > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void computeMarginalReconstruction::outputTheMarginalProbForEachCharForEachNodePos(std::ostream&, int)' at computeMarginalReconstruction.cpp:177:7: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >*, vector > > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void computeMarginalReconstruction::outputTheMarginalProbForEachCharForEachNodePos(std::ostream&, int)' at computeMarginalReconstruction.cpp:177:7: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::computeCoEvolutionScoresBasedOnSimulatedData(sequenceContainer&)': gainLoss.cpp:2484:22: warning: 'countsGL' may be used uninitialized [-Wmaybe-uninitialized] 2484 | countsGL->run(); | ~~~~~~~~~~~~~^~ gainLoss.cpp:2466:26: note: 'countsGL' was declared here 2466 | computeCountsGL* countsGL; | ^~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'computeMarginalReconstruction::computeMarginalReconstruction(const tree&, std::vector&, const sequenceContainer&)' at computeMarginalReconstruction.cpp:24:28: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp In file included from /usr/include/c++/13/vector:72, from ../../libs/phylogeny/definitions.h:18, from computePosteriorExpectationOfChange.h:23: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'Vdouble gainLoss::computeFreq()' at gainLoss.cpp:1147:18: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'Vdouble gainLoss::computeFreq()' at gainLoss.cpp:1148:18: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^~~~~~~~ jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': jointNoGamma.cpp:23:17: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] 23 | MDOUBLE totalLikelihoodOfReconstruction = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ jointNoGamma.cpp: In member function 'std::vector jointNoGamma::computeJointAncestralFromSSC(int, const suffStatGlobalHomPos&, const suffStatGlobalHomPosJointNoGamma&, doubleRep&)': jointNoGamma.cpp:108:33: warning: unused variable 'maxL' [-Wunused-variable] 108 | MDOUBLE maxL = VERYSMALL; | ^~~~ 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; | ^~~~~~~~ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, from optimizeGainLossModelVV.h:27, from optimizeGainLossModelVV.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.h: In constructor 'optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)': optimizeGainLossModelVV.h:82:18: warning: 'optimizeGainLossModelVV::_weightsUniqPatterns' will be initialized after [-Wreorder] 82 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.h:81:27: warning: 'unObservableData* optimizeGainLossModelVV::_unObservableData_p' [-Wreorder] 81 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] 25 | optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, | ^~~~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.cpp:258:41: warning: unused variable 'currentlogL' [-Wunused-variable] 258 | MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); | ^~~~~~~~~~~ optimizeGainLossModelVV.cpp:76:17: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] 76 | MDOUBLE sumPijQij; | ^~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../../libs/phylogeny/definitions.h:18, from jointNoGamma.h:4, from jointNoGamma.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void jointNoGamma::compute()' at jointNoGamma.cpp:37:40: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.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 -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp In file included from mainbb.cpp:31: ../../libs/phylogeny/bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': ../../libs/phylogeny/bestGtrModelParams.h:175:28: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] 175 | stochasticProcess& _sp; | ^~~ ../../libs/phylogeny/bestGtrModelParams.h:173:34: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] 173 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::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; | ^~~ In file included from mainbb.h:4, from mainbb.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const std::string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, from gainLossModel.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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): | ^~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from siteSpecificGL.cpp:23: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from siteSpecificGL.cpp:24: gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../../libs/phylogeny/definitions.h:18, from siteSpecificGL.h:22, from siteSpecificGL.cpp:18: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ 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 /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeEB_EXP_siteSpecificGL(int, const sequenceContainer&, const std::vector >&, const tree&, const distribution*, const distribution*, const distribution*, Vdouble&, double&, double&, double&, double&, double, VVVdouble&, unObservableData*)' at siteSpecificGL.cpp:102:19: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, from computePosteriorExpectationOfChange.cpp:25: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o ar: creating libfastml.a a - fastml.o a - bbAlg.o a - bbComputeDownAlg.o a - bbComputeUpAlg.o a - bbEvaluateSpecificAV.o a - bbfindBestAVDynProg.o a - bbNodeOrderAlg.o a - bb_options.o a - bbReport.o a - computeMarginalReconstruction.o a - jointNoGamma.o a - mainbb.o a - sequenceDataDiff.o a - suffStatComponentJointNoGamma.o ranlib libfastml.a g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml In file included from /usr/include/c++/13/iostream:41, from ../../libs/phylogeny/readTree.h:6, from ../../libs/phylogeny/tree.h:7, from ../../libs/phylogeny/simulateJumpsAbstract.h:5, from ../../libs/phylogeny/simulateJumps.h:4, from computePosteriorExpectationOfChange.h:24, from computePosteriorExpectationOfChange.cpp:17: In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3: /usr/include/c++/13/ostream:223:25: warning: 'Down' may be used uninitialized [-Wmaybe-uninitialized] 223 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': computePosteriorExpectationOfChange.cpp:215:27: note: 'Down' was declared here 215 | doubleRep resDXY, Down, Up; | ^~~~ In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3: /usr/include/c++/13/ostream:223:25: warning: 'Up' may be used uninitialized [-Wmaybe-uninitialized] 223 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ computePosteriorExpectationOfChange.cpp: In member function 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)': computePosteriorExpectationOfChange.cpp:215:33: note: 'Up' was declared here 215 | doubleRep resDXY, Down, Up; | ^~ In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]', inlined from 'double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)' at computePosteriorExpectationOfChange.cpp:230:3: /usr/include/c++/13/ostream:223:25: warning: 'pij' may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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; | ^~~ make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp In file included from gainLoss.h:30, from gainLossProject.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp In file included from gainLoss.h:30, from gainLossOptimizer.h:24, from gainLossOptimizer.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp In file included from gainLossOptimizer.cpp:20: bblLS.h: At global scope: bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 58 | MDOUBLE curL =NULL); | ^~~~ bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:119:27: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:18: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:18: warning: when initialized here [-Wreorder] 96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~ bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:174:27: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:18: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:18: warning: when initialized here [-Wreorder] 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, stochasticProcess*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)': gainLossOptimizer.h:134:14: warning: 'gainLossOptimizer::_tr' will be initialized after [-Wreorder] 134 | tree _tr; | ^~~ gainLossOptimizer.h:109:28: warning: 'stochasticProcess* gainLossOptimizer::_sp' [-Wreorder] 109 | stochasticProcess *_sp; | ^~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, | ^~~~~~~~~~~~~~~~~ gainLossOptimizer.h:135:27: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] 135 | sequenceContainer _sc; | ^~~ gainLossOptimizer.h:93:17: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] 93 | MDOUBLE _epsilonOptimization; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, | ^~~~~~~~~~~~~~~~~ gainLossOptimizer.h:104:18: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] 104 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:28: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] 102 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, | ^~~~~~~~~~~~~~~~~ gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, std::vector >&, distribution*, distribution*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)': gainLossOptimizer.h:139:23: warning: 'gainLossOptimizer::_lossDist' will be initialized after [-Wreorder] 139 | distribution* _lossDist; | ^~~~~~~~~ gainLossOptimizer.h:135:27: warning: 'sequenceContainer gainLossOptimizer::_sc' [-Wreorder] 135 | sequenceContainer _sc; | ^~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, | ^~~~~~~~~~~~~~~~~ gainLossOptimizer.h:135:27: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] 135 | sequenceContainer _sc; | ^~~ gainLossOptimizer.h:93:17: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] 93 | MDOUBLE _epsilonOptimization; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, | ^~~~~~~~~~~~~~~~~ gainLossOptimizer.h:104:18: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] 104 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:28: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] 102 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, | ^~~~~~~~~~~~~~~~~ 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:30, from rate4siteGL.h:24, from rate4siteGL.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp In file included from /usr/include/c++/13/vector:72, from ../../libs/phylogeny/definitions.h:18, from rate4siteGL.h:22: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void rate4siteGL::normalizeRates()' at rate4siteGL.cpp:233:25: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': gainLossOptimizer.cpp:833:16: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] 833 | return res; | ^~~ gainLossOptimizer.cpp:820:43: note: 'res' was declared here 820 | gainLossOptions::distributionType res; | ^~~ In file included from gainLoss.h:30, from computeCountsGL.h:24, from computeCountsGL.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, VVdouble&, double, bool)': computeCountsGL.h:104:14: warning: 'computeCountsGL::_tr' will be initialized after [-Wreorder] 104 | tree _tr; | ^~~ computeCountsGL.h:102:28: warning: 'stochasticProcess* computeCountsGL::_sp' [-Wreorder] 102 | stochasticProcess *_sp; | ^~~ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] 28 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, VVdouble& logLpostPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ computeCountsGL.h:117:17: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] 117 | MDOUBLE _distanceFromNearestOTUForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:14: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] 113 | bool _isSilent; | ^~~~~~~~~ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] 28 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, VVdouble& logLpostPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, std::vector >&, distribution*, distribution*, std::string&, VVVdouble&, double, bool)': computeCountsGL.h:109:23: warning: 'computeCountsGL::_lossDist' will be initialized after [-Wreorder] 109 | distribution* _lossDist; | ^~~~~~~~~ computeCountsGL.h:105:27: warning: 'sequenceContainer computeCountsGL::_sc' [-Wreorder] 105 | sequenceContainer _sc; | ^~~ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] 33 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ computeCountsGL.h:117:17: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] 117 | MDOUBLE _distanceFromNearestOTUForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:14: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] 113 | bool _isSilent; | ^~~~~~~~~ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] 33 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ In file included from gainLoss.h:30, from computeCorrelations.h:25, from computeCorrelations.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)': computeCorrelations.cpp:130:13: warning: unused variable 'numOfbranches' [-Wunused-variable] 130 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node | ^~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': computeCorrelations.cpp:408:29: warning: unused variable 'isHigherNminReducedFreqOfHighCorr' [-Wunused-variable] 408 | int isHigherNminReducedFreqOfHighCorr = false; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:348:21: warning: unused variable 'typeIndex' [-Wunused-variable] 348 | int typeIndex = corIndex % _EventTypes.size(); // in case both Spearman and pearson are used | ^~~~~~~~~ computeCorrelations.cpp: In member function 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)': computeCorrelations.cpp:559:30: warning: NULL used in arithmetic [-Wpointer-arith] 559 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:569:38: warning: NULL used in arithmetic [-Wpointer-arith] 569 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:579:38: warning: NULL used in arithmetic [-Wpointer-arith] 579 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:584:30: warning: NULL used in arithmetic [-Wpointer-arith] 584 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp: In member function 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)': computeCorrelations.cpp:676:37: warning: variable 'prevNumberOfSimulationsInRange' set but not used [-Wunused-but-set-variable] 676 | int prevNumberOfSimulationsInRange = 1; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:677:37: warning: variable 'prevNumberOfSimulationPointsMoreExtremeOrEqToCorr' set but not used [-Wunused-but-set-variable] 677 | int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:679:37: warning: unused variable 'numOfBinsWithLowerSignificance' [-Wunused-variable] 679 | int numOfBinsWithLowerSignificance = 0; // allow 2 "bin-iteration" even with lower significance to mitigate chance of "missing" higher significance in lower bin | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:680:38: warning: unused variable 'isNextLowerBinAllowed' [-Wunused-variable] 680 | bool isNextLowerBinAllowed = true; | ^~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'void computeCorrelations::produceSymeticMatrix(VVVdouble&, bool)': computeCorrelations.cpp:894:26: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 894 | if(!numOfSites_A == numOfSites_B){ | ^~ computeCorrelations.cpp:894:12: note: add parentheses around left hand side expression to silence this warning 894 | if(!numOfSites_A == numOfSites_B){ | ^~~~~~~~~~~~~ | ( ) computeCorrelations.cpp: In member function 'void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::string*)': computeCorrelations.cpp:1009:14: warning: unused variable 'isPearson' [-Wunused-variable] 1009 | bool isPearson = false; | ^~~~~~~~~ computeCorrelations.cpp:1025:13: warning: unused variable 'numOfbranches' [-Wunused-variable] 1025 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node | ^~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)': computeCorrelations.cpp:1347:67: warning: narrowing conversion of 'gainLossOptions::_pValueCutOffForBootStrap' from 'double' to 'float' [-Wnarrowing] 1347 | float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001}; | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:1300:14: warning: variable 'it_siteB' set but not used [-Wunused-but-set-variable] 1300 | it_B it_siteB = it_siteA->second.begin(); | ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from gainLoss.h:75: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from gainLoss.h:30, from gainLoss4site.h:24, from gainLoss4site.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1942:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1942 | __sort(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~ /usr/include/c++/13/bits/stl_algo.h:1942:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'std::pair<_FIter, _FIter> std::__equal_range(_ForwardIterator, _ForwardIterator, const _Tp&, _CompareItTp, _CompareTpIt) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = float; _CompareItTp = __gnu_cxx::__ops::_Iter_less_val; _CompareTpIt = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2110:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2110 | __equal_range(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:2110:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'std::pair<_FIter, _FIter> std::__equal_range(_ForwardIterator, _ForwardIterator, const _Tp&, _CompareItTp, _CompareTpIt) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _CompareItTp = __gnu_cxx::__ops::_Iter_less_val; _CompareTpIt = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/13/bits/stl_algo.h:2110:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:2110:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'std::pair<_FIter, _FIter> std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', inlined from 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)' at computeCorrelations.cpp:564:24: /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2177 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2178 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2179 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'std::pair<_FIter, _FIter> std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = float]', inlined from 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)' at computeCorrelations.cpp:575:24: /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2177 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2178 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2179 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::string&, unObservableData*, double)': gainLoss4site.h:68:14: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] 68 | tree _tr; | ^~~ gainLoss4site.h:61:45: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] 61 | vector > _spVVec; //save stochasticProcess for each category | ^~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, | ^~~~~~~~~~~~~ gainLoss4site.h:79:27: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] 79 | unObservableData* _unObservableData_p; // | ^~~~~~~~~~~~~~~~~~~ gainLoss4site.h:78:17: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] 78 | MDOUBLE _alphaConf; | ^~~~~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, | ^~~~~~~~~~~~~ In function 'std::pair<_FIter, _FIter> std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', inlined from 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)' at computeCorrelations.cpp:564:24: /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2177 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2178 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2179 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'std::pair<_FIter, _FIter> std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = float]', inlined from 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)' at computeCorrelations.cpp:575:24: /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2177 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2178 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2179 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp In file included from /usr/include/c++/13/vector:72, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const extremeValDistribution&}; _Tp = extremeValDistribution; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeCorrelations::produceSortedVectorsOfAllCorrelations(Vdouble&)' at computeCorrelations.cpp:272:27: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeCorrelations::produceSortedVectorsOfAllCorrelations(Vdouble&)' at computeCorrelations.cpp:279:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void computeCorrelations::produceSortedVectorsOfAllCorrelations(Vdouble&)' at computeCorrelations.cpp:294:7: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void computeCorrelations::produceSortedVectorsOfAllCorrelations(Vdouble&)' at computeCorrelations.cpp:294:7: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void computeCorrelations::produceSortedVectorsOfAllCorrelations(Vdouble&)' at computeCorrelations.cpp:298:7: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void computeCorrelations::produceSortedVectorsOfAllCorrelations(Vdouble&)' at computeCorrelations.cpp:298:7: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void computeCorrelations::fillMapValPerPosPerBranch(VVdouble&, std::string, VVVVdouble&, bool, double*)' at computeCorrelations.cpp:1228:45: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void computeCorrelations::fillMapValPerPosPerBranch(VVdouble&, std::string, VVVVdouble&, bool, double*)' at computeCorrelations.cpp:1230:45: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeCorrelations::fillMapValPerPosPerBranch(VVdouble&, std::string, VVVVdouble&, bool, double*)' at computeCorrelations.cpp:1233:44: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from gainLoss.h:30, from simulateChangesAlongTree.cpp:20: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void computeCorrelations::fillMapValPerPosPerBranch(VVdouble&, std::string, VVVVdouble&, bool, double*)' at computeCorrelations.cpp:1233:44: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'std::pair<_FIter, _FIter> std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', inlined from 'void computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMap(VVVdouble&, VVVVdouble&, VVVdouble&)' at computeCorrelations.cpp:848:26: /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2177 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2178 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2179 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'std::pair<_FIter, _FIter> std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', inlined from 'void computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMap(VVVdouble&, VVVVdouble&, VVVdouble&)' at computeCorrelations.cpp:850:26: /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2177 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2178 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2179 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:62, from ../../libs/phylogeny/njConstrain.h:6, from ../../libs/phylogeny/nj.h:11, from gainLoss.h:47: /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: /usr/include/c++/13/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]': /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)' at computeCorrelations.cpp:640:36: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'std::pair<_FIter, _FIter> std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', inlined from 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)' at computeCorrelations.cpp:693:28: /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2177 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2178 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2179 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)' at computeCorrelations.cpp:725:85: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)' at computeCorrelations.cpp:729:99: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)' at computeCorrelations.cpp:729:188: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)' at computeCorrelations.cpp:730:85: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)' at computeCorrelations.cpp:735:92: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In function 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]', inlined from 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)' at computeCorrelations.cpp:761:8: /usr/include/c++/13/bits/stl_algo.h:4861:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 4861 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:30, from simulateOnePos.cpp:32: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: 'virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)' was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by 'gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)' 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:17: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulateOnePos.cpp:18: simulateOnePos.h: In constructor 'simulateOnePos::simulateOnePos(std::string, std::ostream*, std::ostream*, int, std::string, double, double, bool, stochasticProcess*, tree*, Vdouble*, Vdouble*)': simulateOnePos.h:72:14: warning: 'simulateOnePos::_simulateNullModel' will be initialized after [-Wreorder] 72 | bool _simulateNullModel; | ^~~~~~~~~~~~~~~~~~ simulateOnePos.h:63:13: warning: 'int simulateOnePos::_simNum' [-Wreorder] 63 | int _simNum; | ^~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile | ^~~~~~~~~~~~~~ simulateOnePos.h:65:17: warning: 'simulateOnePos::_theta' will be initialized after [-Wreorder] 65 | MDOUBLE _theta; | ^~~~~~ simulateOnePos.h:64:17: warning: 'double simulateOnePos::_sumGainLoss' [-Wreorder] 64 | MDOUBLE _sumGainLoss; | ^~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile | ^~~~~~~~~~~~~~ simulateOnePos.h:75:18: warning: 'simulateOnePos::_freq_cpN' will be initialized after [-Wreorder] 75 | Vdouble* _freq_cpN; | ^~~~~~~~~ simulateOnePos.h:69:18: warning: 'std::ostream* simulateOnePos::_simulatedEvents' [-Wreorder] 69 | ostream *_simulatedEvents; | ^~~~~~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile | ^~~~~~~~~~~~~~ simulateOnePos.cpp: In member function 'void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::string)': simulateOnePos.cpp:181:30: warning: unused variable 'isRevers' [-Wunused-variable] 181 | bool isRevers = false; | ^~~~~~~~ simulateOnePos.cpp:202:33: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] 202 | MDOUBLE sumQii = 1.0; | ^~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)' at computeCorrelations.cpp:1323:93: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)' at computeCorrelations.cpp:1332:21: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)' at computeCorrelations.cpp:1342:15: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)' at computeCorrelations.cpp:1344:7: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)' at computeCorrelations.cpp:1344:7: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'std::pair<_FIter, _FIter> std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = float]', inlined from 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)' at computeCorrelations.cpp:1351:25: /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2177 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2178 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2179 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'std::pair<_FIter, _FIter> std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', inlined from 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)' at computeCorrelations.cpp:1369:24: /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2177 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2178 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2179 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]', inlined from 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)' at computeCorrelations.cpp:1431:68: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)' at computeCorrelations.cpp:1344:7: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)' at computeCorrelations.cpp:201:32: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)' at computeCorrelations.cpp:202:35: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from bblLS.h:27, from bblLS.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bblLS.h:50:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:31: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 58 | MDOUBLE curL =NULL); | ^~~~ bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:119:27: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:18: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:18: warning: when initialized here [-Wreorder] 96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~ bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:174:27: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:18: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:18: warning: when initialized here [-Wreorder] 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, stochasticProcess*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': bblLS.cpp:36:21: warning: NULL used in arithmetic [-Wpointer-arith] 36 | if (curL == NULL) | ^~~~ bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, std::vector >&, const distribution*, const distribution*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': bblLS.cpp:112:21: warning: NULL used in arithmetic [-Wpointer-arith] 112 | if (curL == NULL) | ^~~~ 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 std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', inlined from 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)' at computeCorrelations.cpp:357:24: /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2177 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2178 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2179 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'std::pair<_FIter, _FIter> std::equal_range(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = double]', inlined from 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)' at computeCorrelations.cpp:435:26: /usr/include/c++/13/bits/stl_algo.h:2177:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2177 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2178 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2179 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)' at computeCorrelations.cpp:471:59: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)' at computeCorrelations.cpp:473:59: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)' at computeCorrelations.cpp:475:59: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)' at computeCorrelations.cpp:479:8: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)' at computeCorrelations.cpp:479:8: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = extremeValDistribution; _Alloc = std::allocator]', inlined from 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)' at computeCorrelations.cpp:486:48: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from sankoffReconstructGL.h:29, from sankoffReconstructGL.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: 'virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)' was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by 'generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)' 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)': sankoffReconstructGL.h:85:16: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] 85 | string _outDir; | ^~~~~~~ sankoffReconstructGL.h:84:17: warning: 'double sankoffReconstructGL::_costMatrixGainLossRatio' [-Wreorder] 84 | MDOUBLE _costMatrixGainLossRatio; | ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): | ^~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h:84:17: warning: 'sankoffReconstructGL::_costMatrixGainLossRatio' will be initialized after [-Wreorder] 84 | MDOUBLE _costMatrixGainLossRatio; | ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h:83:17: warning: 'double sankoffReconstructGL::_distanceFromRootForRecent' [-Wreorder] 83 | MDOUBLE _distanceFromRootForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../../libs/phylogeny/definitions.h:18, from ../../libs/phylogeny/tree.h:6, from sankoffReconstructGL.h:23: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'double sankoffReconstructGL::traverseDownMP(VVdouble&, std::vector > >&, VVint&, VVdouble&)' at sankoffReconstructGL.cpp:368:23: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void sankoffReconstructGL::traverseUpMP(VVdouble&, std::vector > >&)' at sankoffReconstructGL.cpp:315:20: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -j3 test make[1]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make test make[2]: Entering directory '/build/reproducible-path/fastml-3.11/libs' cd phylogeny && make test cd programs;make test make[2]: Entering directory '/build/reproducible-path/fastml-3.11/programs' cd fastml && make test cd gainLoss && make test make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' if [ -d tests ] ; then cd tests && make -k ; fi make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' 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/libs/phylogeny' cd tests; make -k test make[4]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny/tests' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. split_test.cpp ../libEvolTree.a -lEvolTree -o split_test 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' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. splitMap_test.cpp ../libEvolTree.a -lEvolTree -o splitMap_test make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqTheDistBetweenThem-3.cpp ../libEvolTree.a -lEvolTree -o given2seqTheDistBetweenThem-3 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistBetweenThem.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistBetweenThem g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. checkTreeLikelihoodGivenBranches.cpp ../libEvolTree.a -lEvolTree -o checkTreeLikelihoodGivenBranches g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistBetweenThemGamma.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistBetweenThemGamma g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistanceK2P.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistanceK2P g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. doubleRep.cpp ../libEvolTree.a -lEvolTree -o doubleRep g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. readTreeWithComments.cpp ../libEvolTree.a -lEvolTree -o readTreeWithComments ./split_test > split_test.out.tmp ./splitMap_test > splitMap_test.out.tmp ./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp ./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp ./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp ./doubleRep > doubleRep.out.tmp diff split_test.out.tmp split_test.out.standard diff splitMap_test.out.tmp splitMap_test.out.standard diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard diff doubleRep.out.tmp doubleRep.out.standard ./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp diff readTreeWithComments.out.tmp readTreeWithComments.out.standard ./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny/tests' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/libs' 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 -j3 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/fastml' mkdir -p ../../bin cp fastml ../../bin/fastml make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' mkdir -p ../../bin cp indelCoder ../../bin/indelCoder make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/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 dpkg-shlibdeps: warning: debian/fastml/usr/bin/indelCoder contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/fastml/usr/bin/gainLoss contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/fastml/usr/bin/fastml contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'fastml' in '../fastml_3.11-4_armhf.deb'. dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.11-4_armhf.deb'. dpkg-genbuildinfo --build=binary -O../fastml_3.11-4_armhf.buildinfo dpkg-genchanges --build=binary -O../fastml_3.11-4_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) 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/28038 and its subdirectories I: Current time: Mon Apr 22 09:22:06 -12 2024 I: pbuilder-time-stamp: 1713820926 Mon Apr 22 21:23:05 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64b-armhf-rb.debian.net. Mon Apr 22 21:23:05 UTC 2024 I: Preparing to do remote build '2' on virt64b-armhf-rb.debian.net. Mon Apr 22 21:35:35 UTC 2024 I: Deleting $TMPDIR on virt64b-armhf-rb.debian.net. Mon Apr 22 21:35:37 UTC 2024 I: fastml_3.11-4_armhf.changes: Format: 1.8 Date: Wed, 24 Jan 2024 17:23:21 +0100 Source: fastml Binary: fastml fastml-dbgsym Architecture: armhf Version: 3.11-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: fastml - maximum likelihood ancestral amino-acid sequence reconstruction Closes: 1044832 Changes: fastml (3.11-4) unstable; urgency=medium . * Fix clean target Closes: #1044832 * Standards-Version: 4.6.2 (routine-update) * d/watch: Upstream download vanished Checksums-Sha1: c8d554fb9204de27d5bb94301e97b16300d0d8c2 16328492 fastml-dbgsym_3.11-4_armhf.deb 290b0deaba4fc691d5469092afa2faff709032a2 5268 fastml_3.11-4_armhf.buildinfo 1df84974c6ab79dec517563acb989a7acd2e4225 788456 fastml_3.11-4_armhf.deb Checksums-Sha256: fda20c4a852377680415f0c015b3ba96d7550a699cead619f23e1cd1ad7cc223 16328492 fastml-dbgsym_3.11-4_armhf.deb 5dbc4391289bf66ef8989aca89d785cb51755517ecc4d17a3e37c2245583d75a 5268 fastml_3.11-4_armhf.buildinfo f2e574b985b13ee26204c61b101411b51ff71c2772b68435d85cbc2f0af78600 788456 fastml_3.11-4_armhf.deb Files: 6675956896c2d10240b2386d843f0f93 16328492 debug optional fastml-dbgsym_3.11-4_armhf.deb 45258b90ca07ce971133435ae52360a8 5268 science optional fastml_3.11-4_armhf.buildinfo 78041151dce6b47c083a133693111f3a 788456 science optional fastml_3.11-4_armhf.deb Mon Apr 22 21:35:39 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_17-3562.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.3foiQUBY/fastml_3.11-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.3foiQUBY/fastml_3.11-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.3foiQUBY/fastml_3.11-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.3foiQUBY/b1/fastml_3.11-4_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.3foiQUBY/b2/fastml_3.11-4_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.504s) 0.504s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.192s) 0.192s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 810ms CPU time consumed: 807ms Mon Apr 22 21:35:40 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Mon Apr 22 21:35:40 UTC 2024 I: fastml from trixie built successfully and reproducibly on armhf. Mon Apr 22 21:35:41 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Apr 22 21:35:41 UTC 2024 I: Submitting 8.0K b1/fastml_3.11-4_armhf.buildinfo.asc Mon Apr 22 21:35:42 UTC 2024 I: Submitting 8.0K b2/fastml_3.11-4_armhf.buildinfo.asc Mon Apr 22 21:35:43 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Apr 22 21:35:43 UTC 2024 I: Done submitting .buildinfo files. Mon Apr 22 21:35:43 UTC 2024 I: Removing signed fastml_3.11-4_armhf.buildinfo.asc files: removed './b1/fastml_3.11-4_armhf.buildinfo.asc' removed './b2/fastml_3.11-4_armhf.buildinfo.asc'