I: pbuilder: network access will be disabled during build I: Current time: Fri Sep 16 16:26:28 -12 2022 I: pbuilder-time-stamp: 1663388788 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_3.11-3.dsc] I: copying [./fastml_3.11.orig.tar.gz] I: copying [./fastml_3.11-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.d2DVRKuu/trustedkeys.kbx': General error gpgv: Signature made Thu Dec 17 02:38:59 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./fastml_3.11-3.dsc dpkg-source: info: extracting fastml in fastml-3.11 dpkg-source: info: unpacking fastml_3.11.orig.tar.gz dpkg-source: info: unpacking fastml_3.11-3.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/27344/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='27344' 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/tmp.Cno4zFGXKi/pbuilderrc_wOum --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Cno4zFGXKi/b1 --logfile b1/build.log fastml_3.11-3.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink9-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 4 2021 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Jul 28 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 28 2021 more -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 16 03:49 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jul 28 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Jul 28 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/27344/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: arm64 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 ... 19646 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} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{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, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 17.9 MB of archives. After unpacking 67.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Fetched 17.9 MB in 1s (12.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../10-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../23-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../25-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:arm64 (0.183-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... 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/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_3.11-3_source.changes dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.11-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/fastml-3.11' dh_auto_clean make -j8 clean make[2]: Entering directory '/build/fastml-3.11' cd libs;make clean cd programs;make clean make[3]: Entering directory '/build/fastml-3.11/libs' cd phylogeny && make clean make[3]: Entering directory '/build/fastml-3.11/programs' cd fastml && make clean cd gainLoss && make clean make[4]: Entering directory '/build/fastml-3.11/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Entering directory '/build/fastml-3.11/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o cd indelCoder && make clean make[4]: Leaving directory '/build/fastml-3.11/libs/phylogeny' make[3]: Leaving directory '/build/fastml-3.11/libs' make[4]: Leaving directory '/build/fastml-3.11/programs/fastml' make[4]: Entering directory '/build/fastml-3.11/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Entering directory '/build/fastml-3.11/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Leaving directory '/build/fastml-3.11/programs/indelCoder' make[4]: Leaving directory '/build/fastml-3.11/programs/gainLoss' make[3]: Leaving directory '/build/fastml-3.11/programs' make[2]: Leaving directory '/build/fastml-3.11' rm -f libs/phylogeny/make.dep \ programs/fastml/make.dep \ programs/gainLoss/make.dep \ programs/indelCoder/make.dep make[1]: Leaving directory '/build/fastml-3.11' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/fastml-3.11' cd libs;make all make[2]: Entering directory '/build/fastml-3.11/libs' cd phylogeny && make all make[3]: Entering directory '/build/fastml-3.11/libs/phylogeny' making depend g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o AddLog.o AddLog.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiProp.o NNiProp.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiSep.o NNiSep.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Nni.o Nni.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o aaJC.o aaJC.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTrees.o allTrees.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o alphabet.o alphabet.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o amino.o amino.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlpha.o bestAlpha.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -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:371:10: 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:184:10: warning: variable 'ax' set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ bestAlphaManyTrees.cpp:184:13: warning: variable 'bx' set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ bestAlphaManyTrees.cpp:184:16: 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 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o clustalFormat.o clustalFormat.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeCounts.o computeCounts.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeDownAlg.o computeDownAlg.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeMarginalAlg.o computeMarginalAlg.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlg.o computeUpAlg.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -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:57:12: warning: 'computeSubstitutionCounts::_LpostPerSpPerCat' will be initialized after [-Wreorder] 57 | VVVdouble _LpostPerSpPerCat; // _LpostPerSpPerCat[sp][rateCat][pos] | ^~~~~~~~~~~~~~~~~ computeSubstitutionCounts.h:53:6: 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): | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from computeSubstitutionCounts.cpp:1: computeSubstitutionCounts.h:54:10: warning: 'computeSubstitutionCounts::_probCutOffSum' will be initialized after [-Wreorder] 54 | MDOUBLE _probCutOffSum; | ^~~~~~~~~~~~~~ computeSubstitutionCounts.h:52:7: warning: 'bool computeSubstitutionCounts::_isSilent' [-Wreorder] 52 | bool _isSilent; | ^~~~~~~~~ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 15 | computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.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:29:12: warning: 'fromCountTableComponentToDistancePropEB::_nodeID' will be initialized after [-Wreorder] 29 | const int _nodeID; | ^~~~~~~ fromCountTableComponentToDistancePropEB.h:28:27: 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 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)': goldmanYangModel.cpp:8:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] 8 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV): | ^~~~~~~~~~~~~~~~ goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, const Vdouble&, bool)': goldmanYangModel.cpp:18:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] 18 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): | ^~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.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:274:18: required from here likeDist.cpp:210:13: warning: variable 'oldIntervalSize' set but not used [-Wunused-but-set-variable] 210 | MDOUBLE oldIntervalSize = currentIntervalSize; | ^~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o molphyFormat.o molphyFormat.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -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;igetNumberOfSons()+2); // both s1 and s2 should have been skiped | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readTree.o readTree.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o recognizeFormat.o recognizeFormat.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModel.o replacementModel.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o searchStatus.o searchStatus.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequence.o sequence.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequenceContainer.o sequenceContainer.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o siteSpecificRate.o siteSpecificRate.cpp sequence.cpp: In constructor 'sequence::sequence(const sequence&, const alphabet*)': sequence.cpp:76:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 76 | || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp sequenceContainer.cpp: In member function 'void sequenceContainer::removeGapPositions()': sequenceContainer.cpp:187:7: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] 187 | bool gapCol; | ^~~~~~ sequenceContainer.cpp: In member function 'void sequenceContainer::removeGapPositionsAllSeqs()': sequenceContainer.cpp:199:7: 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:452:12: 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:467:12: warning: unused variable 'len' [-Wunused-variable] 467 | const int len = _seqDataVec[0].seqLen(); | ^~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o split.o split.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcess.o stochasticProcess.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp tree.cpp: In constructor 'tree::tree(const string&)': tree.cpp:180:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 180 | if (in.is_open()) | ^~ tree.cpp:182:3: 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 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp treeUtil.cpp: In function 'std::vector getNexusTreesFromFile(const string&)': treeUtil.cpp:371:25: warning: variable 'itStrStart' set but not used [-Wunused-but-set-variable] 371 | string::const_iterator itStrStart = it->begin(); | ^~~~~~~~~~ treeUtil.cpp:372:25: warning: variable 'itStrEnd' set but not used [-Wunused-but-set-variable] 372 | string::const_iterator itStrEnd = it->end(); | ^~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.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:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] 175 | stochasticProcess& _sp; | ^~~ bestGtrModelParams.h:173:27: 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 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistribution.o betaDistribution.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp In file included from betaDistribution.cpp:3: betaDistribution.h: In copy constructor 'betaDistribution::betaDistribution(const betaDistribution&)': betaDistribution.h:54:18: warning: 'betaDistribution::_boundary' will be initialized after [-Wreorder] 54 | vector _boundary; | ^~~~~~~~~ betaDistribution.h:47:10: 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 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o extremeValDistribution.o extremeValDistribution.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeJumps.o computeJumps.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp In file included from computeJumps.cpp:1: computeJumps.h: In constructor 'computeJumps::gFunc::gFunc(double, double, double)': computeJumps.h:59:11: warning: 'computeJumps::gFunc::_Lambda2' will be initialized after [-Wreorder] 59 | MDOUBLE _Lambda2; | ^~~~~~~~ computeJumps.h:57:11: 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:141:18: warning: unused variable 'pAlph' [-Wunused-variable] 141 | const alphabet* pAlph = sc.getAlphabet(); | ^~~~~ suffStatGammaMixture.cpp: In member function 'void suffStatGammaMixture::computeStatistics()': suffStatGammaMixture.cpp:123:12: 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:224:11: warning: unused variable 'first' [-Wunused-variable] 224 | MDOUBLE first = _MkVec[comp] * log(P_k); | ^~~~~ suffStatGammaMixture.cpp:225:11: warning: unused variable 'second' [-Wunused-variable] 225 | MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k); | ^~~~~~ suffStatGammaMixture.cpp:226:11: warning: unused variable 'third' [-Wunused-variable] 226 | MDOUBLE third = -_MkVec[comp] * gammln(alpha_k); | ^~~~~ suffStatGammaMixture.cpp:227:11: warning: unused variable 'fourth' [-Wunused-variable] 227 | MDOUBLE fourth = -_AkVec[comp]*beta_k; | ^~~~~~ suffStatGammaMixture.cpp:228:11: warning: unused variable 'fifth' [-Wunused-variable] 228 | MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0); | ^~~~~ suffStatGammaMixture.cpp:216:10: warning: variable 'res2' set but not used [-Wunused-but-set-variable] 216 | MDOUBLE res2 = 0.0; | ^~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp In file included from GamMixtureOptimizer.cpp:3: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': optGammaMixtureEM.h:76:11: 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:87:11: warning: unused variable 'debugRes' [-Wunused-variable] 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); | ^~~~~~~~ In file included from optGammaMixtureEM.cpp:1: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': optGammaMixtureEM.h:76:11: 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:87:11: warning: unused variable 'debugRes' [-Wunused-variable] 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); | ^~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2codon.o bblEM2codon.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndK.o bestAlphaAndK.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gtrModel.o gtrModel.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestGtrModelParams.o bestGtrModelParams.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -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:54:10: warning: 'gtrModel::_g2t' will be initialized after [-Wreorder] 54 | MDOUBLE _g2t; | ^~~~ gtrModel.h:47:10: 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:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] 175 | stochasticProcess& _sp; | ^~~ bestGtrModelParams.h:173:27: 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 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o integerAlphabet.o integerAlphabet.cpp gtrModel.cpp: In member function 'double gtrModel::get_a2c() const': gtrModel.cpp:139:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] 139 | return result; | ^~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_a2g() const': gtrModel.cpp:153:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] 153 | return result; | ^~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_a2t() const': gtrModel.cpp:167:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] 167 | return result; | ^~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_c2g() const': gtrModel.cpp:181:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] 181 | return result; | ^~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_c2t() const': gtrModel.cpp:195:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] 195 | return result; | ^~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_g2t() const': gtrModel.cpp:209:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] 209 | return result; | ^~~~~~ ar rv libEvolTree.a AddLog.o NNiProp.o NNiSep.o Nni.o aaJC.o allTrees.o allTreesSeparateModel.o alphabet.o amino.o bestAlpha.o bestAlphaManyTrees.o bestHKYparam.o bootstrap.o bblEM.o bblEMfixRoot.o bblEMProprtional.o bblEMProportionalEB.o bblLSProportionalEB.o bblEMSeperate.o chebyshevAccelerator.o clustalFormat.o codon.o codonJC.o computeCounts.o computeDownAlg.o computeMarginalAlg.o computePijComponent.o computeUpAlg.o computeUpAlgFactors.o computeSubstitutionCounts.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o ConversionUtils.o countTableComponent.o datMatrixHolder.o distanceTable.o distribution.o errorMsg.o evaluateCharacterFreq.o fastStartTree.o fastaFormat.o findRateOfGene.o fromCountTableComponentToDistance.o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistancePropEB.o fromQtoPt.o generalGammaDistributionFixedCategories.o gammaDistribution.o gammaUtilities.o generalGammaDistribution.o getRandomWeights.o goldmanYangModel.o granthamChemicalDistances.o hky.o simulateWithDependence.o KH_calculation.o likeDist.o likeDistfixRoot.o likeDistProp.o likeDistPropEB.o likelihoodComputation.o likelihoodComputationFactors.o logFile.o maseFormat.o molphyFormat.o nexusFormat.o nj.o njConstrain.o nucJC.o nucleotide.o numRec.o Parameters.o phylipFormat.o pijAccelerator.o readDatMatrix.o readTree.o recognizeFormat.o replacementModel.o searchStatus.o seqContainerTreeMap.o sequence.o sequenceContainer.o simulateTree.o siteSpecificRate.o someUtil.o split.o splitMap.o splitTreeUtil.o stochasticProcess.o suffStatComponent.o talRandom.o tree.o treeIt.o treeUtil.o uniDistribution.o uniformDistribution.o cmdline2EvolObjs.o generalGammaDistributionLaguerre.o gammaDistributionLaguerre.o GLaguer.o givenRatesMLDistance.o distanceBasedSeqs2Tree.o posteriorDistance.o pairwiseGammaDistance.o doubleRep.o logRep.o indel.o indelModel.o mulAlphabet.o replacementModelSSRV.o stochasticProcessSSRV.o bestAlphaAndNu.o C_evalParamUSSRV.o matrixUtils.o betaOmegaDistribution.o betaUtilities.o betaDistribution.o geneticCodeHolder.o samplingSequences.o bblEM2USSRV.o bestParamUSSRV.o likeDist2USSRV.o ussrvModel.o likelihoodComputation2USSRV.o fromCountTableComponentToDistance2USSRV.o normalDist.o tamura92.o bestTamura92param.o phylipSequentialFormat.o simulateCodonsJumps.o simulateJumpsAbstract.o ssrvDistanceSeqs2Tree.o multipleStochasticProcess.o distributionPlusInvariant.o extremeValDistribution.o gammaDistributionFixedCategories.o generalGammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.o distributionPlusCategory.o simulateJumps.o computeJumps.o seqeuncesFilter.o optGammaMixtureLS.o mixtureDistribution.o suffStatGammaMixture.o GamMixtureOptimizer.o optGammaMixtureEM.o gainLossAlphabet.o wYangModel.o codonUtils.o likelihoodComputation2Codon.o likeDist2Codon.o unObservableData.o likelihoodComputationGL.o threeStateModel.o threeStateAlphabet.o oneTwoMoreModel.o betaDistributionFixedCategories.o betaDistributionFixedCategoriesWithOmegaUniform.o bblEM2codon.o bestAlphaAndK.o fromCountTableComponentToDistance2Codon.o gtrModel.o bestGtrModelParams.o simulateRateShiftJumps.o integerAlphabet.o ar: creating libEvolTree.a a - AddLog.o a - NNiProp.o a - NNiSep.o a - Nni.o a - aaJC.o a - allTrees.o a - allTreesSeparateModel.o a - alphabet.o a - amino.o a - bestAlpha.o a - bestAlphaManyTrees.o a - bestHKYparam.o a - bootstrap.o a - bblEM.o a - bblEMfixRoot.o a - bblEMProprtional.o a - bblEMProportionalEB.o a - bblLSProportionalEB.o a - bblEMSeperate.o a - chebyshevAccelerator.o a - clustalFormat.o a - codon.o a - codonJC.o a - computeCounts.o a - computeDownAlg.o a - computeMarginalAlg.o a - computePijComponent.o a - computeUpAlg.o a - computeUpAlgFactors.o a - computeSubstitutionCounts.o a - computePosteriorExpectationOfSubstitutions.o a - computePosteriorExpectationOfSubstitutions_nonReversibleSp.o a - ConversionUtils.o a - countTableComponent.o a - datMatrixHolder.o a - distanceTable.o a - distribution.o a - errorMsg.o a - evaluateCharacterFreq.o a - fastStartTree.o a - fastaFormat.o a - findRateOfGene.o a - fromCountTableComponentToDistance.o a - fromCountTableComponentToDistancefixRoot.o a - fromCountTableComponentToDistanceProp.o a - fromCountTableComponentToDistancePropEB.o a - fromQtoPt.o a - generalGammaDistributionFixedCategories.o a - gammaDistribution.o a - gammaUtilities.o a - generalGammaDistribution.o a - getRandomWeights.o a - goldmanYangModel.o a - granthamChemicalDistances.o a - hky.o a - simulateWithDependence.o a - KH_calculation.o a - likeDist.o a - likeDistfixRoot.o a - likeDistProp.o a - likeDistPropEB.o a - likelihoodComputation.o a - likelihoodComputationFactors.o a - logFile.o a - maseFormat.o a - molphyFormat.o a - nexusFormat.o a - nj.o a - njConstrain.o a - nucJC.o a - nucleotide.o a - numRec.o a - Parameters.o a - phylipFormat.o a - pijAccelerator.o a - readDatMatrix.o a - readTree.o a - recognizeFormat.o a - replacementModel.o a - searchStatus.o a - seqContainerTreeMap.o a - sequence.o a - sequenceContainer.o a - simulateTree.o a - siteSpecificRate.o a - someUtil.o a - split.o a - splitMap.o a - splitTreeUtil.o a - stochasticProcess.o a - suffStatComponent.o a - talRandom.o a - tree.o a - treeIt.o a - treeUtil.o a - uniDistribution.o a - uniformDistribution.o a - cmdline2EvolObjs.o a - generalGammaDistributionLaguerre.o a - gammaDistributionLaguerre.o a - GLaguer.o a - givenRatesMLDistance.o a - distanceBasedSeqs2Tree.o a - posteriorDistance.o a - pairwiseGammaDistance.o a - doubleRep.o a - logRep.o a - indel.o a - indelModel.o a - mulAlphabet.o a - replacementModelSSRV.o a - stochasticProcessSSRV.o a - bestAlphaAndNu.o a - C_evalParamUSSRV.o a - matrixUtils.o a - betaOmegaDistribution.o a - betaUtilities.o a - betaDistribution.o a - geneticCodeHolder.o a - samplingSequences.o a - bblEM2USSRV.o a - bestParamUSSRV.o a - likeDist2USSRV.o a - ussrvModel.o a - likelihoodComputation2USSRV.o a - fromCountTableComponentToDistance2USSRV.o a - normalDist.o a - tamura92.o a - bestTamura92param.o a - phylipSequentialFormat.o a - simulateCodonsJumps.o a - simulateJumpsAbstract.o a - ssrvDistanceSeqs2Tree.o a - multipleStochasticProcess.o a - distributionPlusInvariant.o a - extremeValDistribution.o a - gammaDistributionFixedCategories.o a - generalGammaDistributionPlusInvariant.o a - gammaDistributionPlusInvariant.o a - distributionPlusCategory.o a - simulateJumps.o a - computeJumps.o a - seqeuncesFilter.o a - optGammaMixtureLS.o a - mixtureDistribution.o a - suffStatGammaMixture.o a - GamMixtureOptimizer.o a - optGammaMixtureEM.o a - gainLossAlphabet.o a - wYangModel.o a - codonUtils.o a - likelihoodComputation2Codon.o a - likeDist2Codon.o a - unObservableData.o a - likelihoodComputationGL.o a - threeStateModel.o a - threeStateAlphabet.o a - oneTwoMoreModel.o a - betaDistributionFixedCategories.o a - betaDistributionFixedCategoriesWithOmegaUniform.o a - bblEM2codon.o a - bestAlphaAndK.o a - fromCountTableComponentToDistance2Codon.o a - gtrModel.o a - bestGtrModelParams.o a - simulateRateShiftJumps.o a - integerAlphabet.o ranlib libEvolTree.a make[3]: Leaving directory '/build/fastml-3.11/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.11/libs' cd programs;make all make[2]: Entering directory '/build/fastml-3.11/programs' cd fastml && make all cd gainLoss && make all cd indelCoder && make all make[3]: Entering directory '/build/fastml-3.11/programs/fastml' make[3]: Entering directory '/build/fastml-3.11/programs/gainLoss' making depend make[3]: Entering directory '/build/fastml-3.11/programs/indelCoder' making depend making depend g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoder.o indelCoder.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o character.o character.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': indelCoder.cpp:422:6: warning: unused variable 'gapNum' [-Wunused-variable] 422 | int gapNum = 1; | ^~~~~~ character.cpp: In member function 'int character::getLongestGapStIndex()': character.cpp:28:9: warning: 'longestGapStIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] 28 | return longestGapStIndex; | ^~~~~~~~~~~~~~~~~ indelCoder.cpp: In member function 'void indelCoder::printIndelSummary()': indelCoder.cpp:587:7: warning: unused variable 'isSIC' [-Wunused-variable] 587 | bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; | ^~~~~ indelCoder.cpp:597:6: warning: unused variable 'seqLeng' [-Wunused-variable] 597 | int seqLeng = _sc.seqLen(); | ^~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp In file included from bbAlg.h:8, from bbAlg.cpp:1: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ In file included from bbAlg.cpp:1: bbAlg.h: In constructor 'bbAlg::bbAlg(const tree&, std::vector&, const sequenceContainer&, bbAlg::boundMethod, const string&, double, const distribution*)': bbAlg.h:61:16: warning: 'bbAlg::_reportFileName' will be initialized after [-Wreorder] 61 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbAlg.h:60:20: 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, | ^~~~~ In file included from bbAlg.cpp:1: bbAlg.h:60:20: warning: 'bbAlg::BandBReportAllPos1' will be initialized after [-Wreorder] 60 | BandBReportAllPos BandBReportAllPos1; // report for all positions. | ^~~~~~~~~~~~~~~~~~ bbAlg.h:29:14: 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, | ^~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp In file included from bbAlg.h:8, from fastml.cpp:254: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp In file included from mainbb.h:4, from fastml.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ In file included from bbNodeOrderAlg.h:5, from bbAlg.h:5, from bbAlg.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp In file included from gainLossUtils.cpp:19: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:35, from gainLoss.cpp:20: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossUtils.cpp: In function 'void printTreeWithValuesAsBP(std::ostream&, tree::TreeNode* const&, Vstring, VVVdouble*, bool)': gainLossUtils.cpp:72:5: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 72 | if(probs) | ^ gainLossUtils.cpp:88:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 88 | if(probs) | ^ gainLossUtils.cpp: In function 'void updateGainBeta(double, std::vector >&, distribution*, distribution*, bool)': gainLossUtils.cpp:481:10: warning: variable 'normFactor' set but not used [-Wunused-but-set-variable] 481 | MDOUBLE normFactor; | ^~~~~~~~~~ In file included from optimizeGainLossModel.h:27, from optimizeGainLossModel.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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 optimizeGainLossModelVV.h:27, from optimizeGainLossModelVV.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': gainLossUtils.cpp:788:10: warning: unused variable 'scale' [-Wunused-variable] 788 | MDOUBLE scale; | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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 optimizeGainLossModel.cpp:17: optimizeGainLossModel.h: In constructor 'optimizeGainLossModel::optimizeGainLossModel(const tree&, stochasticProcess&, const sequenceContainer&, bool, double, int, Vdouble*, unObservableData*)': optimizeGainLossModel.h:87:11: warning: 'optimizeGainLossModel::_weightsUniqPatterns' will be initialized after [-Wreorder] 87 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.h:86:20: 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, | ^~~~~~~~~~~~~~~~~~~~~ In file included from optimizeGainLossModelVV.cpp:17: optimizeGainLossModelVV.h: In constructor 'optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)': optimizeGainLossModelVV.h:82:11: warning: 'optimizeGainLossModelVV::_weightsUniqPatterns' will be initialized after [-Wreorder] 82 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.h:81:20: 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, | ^~~~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.cpp:85:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] 85 | MDOUBLE sumPijQij; | ^~~~~~~~~ optimizeGainLossModelVV.cpp:258:13: warning: unused variable 'currentlogL' [-Wunused-variable] 258 | MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); | ^~~~~~~~~~~ optimizeGainLossModelVV.cpp:76:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] 76 | MDOUBLE sumPijQij; | ^~~~~~~~~ In file included from gainLoss.cpp:41: bblLS.h: At global scope: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:17: 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:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:11: 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:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:11: warning: when initialized here [-Wreorder] 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.cpp:20: gainLoss.h: In constructor 'gainLoss::gainLoss()': gainLoss.h:266:21: warning: 'gainLoss::_unObservableData_p' will be initialized after [-Wreorder] 266 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ gainLoss.h:240:16: 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) | ^~~~~~~~ In file included from gainLoss.cpp:20: gainLoss.h:240:16: warning: 'gainLoss::_lossDist' will be initialized after [-Wreorder] 240 | distribution* _lossDist; | ^~~~~~~~~ gainLoss.h:239:16: 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) | ^~~~~~~~ In file included from gainLoss.cpp:20: gainLoss.h:273:12: warning: 'gainLoss::_refSeq' will be initialized after [-Wreorder] 273 | sequence* _refSeq; // the reference sequence | ^~~~~~~ gainLoss.h:267:11: 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:604:7: warning: unused variable 'missigDataChar' [-Wunused-variable] 604 | char missigDataChar = -2; | ^~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': gainLoss.cpp:1245:57: 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:1245:38: 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:1868:11: 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:1990:11: warning: unused variable 'sumPijQij' [-Wunused-variable] 1990 | MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); | ^~~~~~~~~ gainLoss.cpp: In member function 'double gainLoss::computeDistanceFromRootForRecent(tree&)': gainLoss.cpp:4205:7: 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:4283:7: 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:4382:19: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ | ^ gainLoss.cpp:4382:7: 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:4951:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] 4951 | MDOUBLE sumQii = 1.0; | ^~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': gainLossUtils.cpp:312:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] 312 | return res; | ^~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp indelCoder.cpp: In member function 'void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)': indelCoder.cpp:175:19: warning: 'condition' may be used uninitialized in this function [-Wmaybe-uninitialized] 175 | while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const string&)': gainLossOptions.cpp:2064:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] 2064 | return returnType; | ^~~~~~~~~~ gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const string&)': gainLossOptions.cpp:2111:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] 2111 | return returnType; | ^~~~~~~~~~ In file included from bbEvaluateSpecificAV.cpp:1: bbEvaluateSpecificAV.h: In constructor 'bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&)': bbEvaluateSpecificAV.h:34:27: warning: 'bbEvaluateSpecificAV::_sc' will be initialized after [-Wreorder] 34 | const sequenceContainer& _sc; | ^~~ bbEvaluateSpecificAV.h:31:23: 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:65:12: warning: unused variable 'rate' [-Wunused-variable] 65 | MDOUBLE rate = _sp.rates(categor); // the r. | ^~~~ In file included from bbEvaluateSpecificAV.h:4, from bbEvaluateSpecificAV.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp In file included from gainLossModel.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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:108:10: warning: 'gainLossModel::_gain' will be initialized after [-Wreorder] 108 | MDOUBLE _gain; // _Q[0][1] | ^~~~~ gainLossModel.h:105:10: 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): | ^~~~~~~~~~~~~ In file included from gainLossModel.cpp:17: gainLossModel.h:112:7: warning: 'gainLossModel::_isRootFreqEQstationary' will be initialized after [-Wreorder] 112 | bool _isRootFreqEQstationary; | ^~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:111:7: 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): | ^~~~~~~~~~~~~ In file included from gainLossModel.cpp:17: gainLossModel.h:114:7: warning: 'gainLossModel::_isHGT_with_Q' will be initialized after [-Wreorder] 114 | bool _isHGT_with_Q; | ^~~~~~~~~~~~~ gainLossModel.h:110:8: 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): | ^~~~~~~~~~~~~ In file included from bbfindBestAVDynProg.h:5, from bbfindBestAVDynProg.cpp:1: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ In file included from bbNodeOrderAlg.cpp:1: bbNodeOrderAlg.h: In constructor 'bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)': bbNodeOrderAlg.h:33:27: warning: 'bbNodeOrderAlg::_sc' will be initialized after [-Wreorder] 33 | const sequenceContainer& _sc; | ^~~ bbNodeOrderAlg.h:32:23: 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, | ^~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bb_options.o bb_options.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp In file included from bbNodeOrderAlg.h:5, from bbNodeOrderAlg.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ 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 siteSpecificGL.cpp:24: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/fastml-3.11/programs/indelCoder' g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp In file included from bb_options.cpp:2: bb_options.h: In constructor 'bb_options::bb_options(int&, char**)': bb_options.h:49:9: warning: 'bb_options::reportFile' will be initialized after [-Wreorder] 49 | string reportFile; | ^~~~~~~~~~ bb_options.h:44:9: 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[]): | ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:45:9: warning: 'bb_options::outFile_seq_marginal' will be initialized after [-Wreorder] 45 | string outFile_seq_marginal; | ^~~~~~~~~~~~~~~~~~~~ bb_options.h:42:9: 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[]): | ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:43:9: warning: 'bb_options::outFile_prob_marginal' will be initialized after [-Wreorder] 43 | string outFile_prob_marginal; | ^~~~~~~~~~~~~~~~~~~~~ bb_options.h:24:9: 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[]): | ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:30:21: warning: 'bb_options::distributionName' will be initialized after [-Wreorder] 30 | distributionsNames distributionName; | ^~~~~~~~~~~~~~~~ bb_options.h:26:16: 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[]): | ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:41:9: warning: 'bb_options::outTreeFileAncestor' will be initialized after [-Wreorder] 41 | string outTreeFileAncestor; | ^~~~~~~~~~~~~~~~~~~ bb_options.h:32:15: 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[]): | ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:47:10: warning: 'bb_options::gammaPar' will be initialized after [-Wreorder] 47 | MDOUBLE gammaPar; | ^~~~~~~~ bb_options.h:28:7: 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[]): | ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:48:6: warning: 'bb_options::gammaCategies' will be initialized after [-Wreorder] 48 | int gammaCategies; | ^~~~~~~~~~~~~ bb_options.h:36:19: 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[]): | ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:39:7: warning: 'bb_options::useChebyshev' will be initialized after [-Wreorder] 39 | bool useChebyshev; | ^~~~~~~~~~~~ bb_options.h:27:9: warning: 'std::string bb_options::treeOutFile' [-Wreorder] 27 | string treeOutFile; | ^~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ In file included from computePosteriorExpectationOfChange.cpp:25: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp In file included from gainLoss.h:35, from gainLossProject.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp In file included from bbReport.cpp:1: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ In file included from gainLoss.h:35, from gainLossOptimizer.h:24, from gainLossOptimizer.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ bbReport.h: In constructor 'BandBReport::BandBReport(const string&, int, int)': bbReport.h:53:16: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder] 53 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:51:12: 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 gainLossOptimizer.cpp:20: bblLS.h: At global scope: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:17: 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:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:11: 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:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:11: warning: when initialized here [-Wreorder] 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, stochasticProcess*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)': gainLossOptimizer.h:134:7: warning: 'gainLossOptimizer::_tr' will be initialized after [-Wreorder] 134 | tree _tr; | ^~~ gainLossOptimizer.h:109:21: 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, | ^~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: gainLossOptimizer.h:135:20: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] 135 | sequenceContainer _sc; | ^~~ gainLossOptimizer.h:93:10: 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, | ^~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: gainLossOptimizer.h:104:11: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] 104 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:21: 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, | ^~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: 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:139:16: warning: 'gainLossOptimizer::_lossDist' will be initialized after [-Wreorder] 139 | distribution* _lossDist; | ^~~~~~~~~ gainLossOptimizer.h:135:20: 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, | ^~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: gainLossOptimizer.h:135:20: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] 135 | sequenceContainer _sc; | ^~~ gainLossOptimizer.h:93:10: 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, | ^~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: gainLossOptimizer.h:104:11: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] 104 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:21: 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, | ^~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengths(int)': gainLossOptimizer.cpp:498:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] 498 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:543:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] 543 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:487:10: 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:634:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] 634 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:677:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] 677 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:623:10: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] 623 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': computeMarginalReconstruction.cpp:67:11: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] 67 | MDOUBLE likelihoodOfPos = 0; | ^~~~~~~~~~~~~~~ computeMarginalReconstruction.cpp:45:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:35, from rate4siteGL.h:24, from rate4siteGL.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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 rate4siteGL.cpp:17: rate4siteGL.h: In constructor 'rate4siteGL::rate4siteGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, unObservableData*)': rate4siteGL.h:59:7: warning: 'rate4siteGL::_tr' will be initialized after [-Wreorder] 59 | tree _tr; | ^~~ rate4siteGL.h:58:21: 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:151:6: warning: unused variable 'precisionHigh' [-Wunused-variable] 151 | int precisionHigh = 5; | ^~~~~~~~~~~~~ rate4siteGL.cpp:152:6: warning: unused variable 'precisionLow' [-Wunused-variable] 152 | int precisionLow = 3; | ^~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': gainLoss.cpp:2035:44: warning: 'bestLossProbInvariant' may be used uninitialized in this function [-Wmaybe-uninitialized] 2035 | if(probInvariant) updateLossProbInvariant(bestLossProbInvariant,lossDist); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': jointNoGamma.cpp:23:10: 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:108:12: warning: unused variable 'maxL' [-Wunused-variable] 108 | MDOUBLE maxL = VERYSMALL; | ^~~~ gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const string&)': gainLossOptions.cpp:2419:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] 2419 | return returnType; | ^~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp In file included from gainLoss.h:35, from computeCountsGL.h:24, from computeCountsGL.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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 computeCountsGL.cpp:17: computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, VVdouble&, double, bool)': computeCountsGL.h:104:7: warning: 'computeCountsGL::_tr' will be initialized after [-Wreorder] 104 | tree _tr; | ^~~ computeCountsGL.h:102:21: 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): | ^~~~~~~~~~~~~~~ In file included from computeCountsGL.cpp:17: computeCountsGL.h:117:10: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] 117 | MDOUBLE _distanceFromNearestOTUForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:7: 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): | ^~~~~~~~~~~~~~~ In file included from computeCountsGL.cpp:17: computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, std::vector >&, distribution*, distribution*, std::string&, VVVdouble&, double, bool)': computeCountsGL.h:109:16: warning: 'computeCountsGL::_lossDist' will be initialized after [-Wreorder] 109 | distribution* _lossDist; | ^~~~~~~~~ computeCountsGL.h:105:20: 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): | ^~~~~~~~~~~~~~~ In file included from computeCountsGL.cpp:17: computeCountsGL.h:117:10: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] 117 | MDOUBLE _distanceFromNearestOTUForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:7: 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:35, from gainLoss4site.h:24, from gainLoss4site.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:35, from computeCorrelations.h:25, from computeCorrelations.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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 gainLoss4site.cpp:17: gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::string&, unObservableData*, double)': gainLoss4site.h:68:7: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] 68 | tree _tr; | ^~~ gainLoss4site.h:61:38: 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, | ^~~~~~~~~~~~~ In file included from gainLoss4site.cpp:17: gainLoss4site.h:79:20: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] 79 | unObservableData* _unObservableData_p; // | ^~~~~~~~~~~~~~~~~~~ gainLoss4site.h:78:10: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] 78 | MDOUBLE _alphaConf; | ^~~~~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, | ^~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)': computeCorrelations.cpp:130:6: 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:408:8: warning: unused variable 'isHigherNminReducedFreqOfHighCorr' [-Wunused-variable] 408 | int isHigherNminReducedFreqOfHighCorr = false; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:348:7: 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:559:23: warning: NULL used in arithmetic [-Wpointer-arith] 559 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:569:24: warning: NULL used in arithmetic [-Wpointer-arith] 569 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:579:24: warning: NULL used in arithmetic [-Wpointer-arith] 579 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:584:23: 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:676:9: warning: variable 'prevNumberOfSimulationsInRange' set but not used [-Wunused-but-set-variable] 676 | int prevNumberOfSimulationsInRange = 1; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:677:9: warning: variable 'prevNumberOfSimulationPointsMoreExtremeOrEqToCorr' set but not used [-Wunused-but-set-variable] 677 | int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:679:9: 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:680:10: warning: unused variable 'isNextLowerBinAllowed' [-Wunused-variable] 680 | bool isNextLowerBinAllowed = true; | ^~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'void computeCorrelations::produceSymeticMatrix(VVVdouble&, bool)': computeCorrelations.cpp:894:19: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 894 | if(!numOfSites_A == numOfSites_B){ | ^~ computeCorrelations.cpp:894:5: 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:1009:7: warning: unused variable 'isPearson' [-Wunused-variable] 1009 | bool isPearson = false; | ^~~~~~~~~ computeCorrelations.cpp:1025:6: 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:1347:53: 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:1300:7: warning: variable 'it_siteB' set but not used [-Wunused-but-set-variable] 1300 | it_B it_siteB = it_siteA->second.begin(); | ^~~~~~~~ gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': gainLossOptimizer.cpp:833:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] 833 | return res; | ^~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()': gainLoss.cpp:3980:52: warning: 'AlphaLoss' may be used uninitialized in this function [-Wmaybe-uninitialized] 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); | ~~~~~~~~~~^~~~~~~~~~~ gainLoss.cpp:3980:52: warning: 'AlphaGain' may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp In file included from bbAlg.h:8, from mainbb.cpp:5: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ In file included from mainbb.cpp:31: ../../libs/phylogeny/bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': ../../libs/phylogeny/bestGtrModelParams.h:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] 175 | stochasticProcess& _sp; | ^~~ ../../libs/phylogeny/bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] 173 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:35, from simulateChangesAlongTree.cpp:20: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp In file included from mainbb.h:4, from mainbb.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp In file included from gainLoss.h:35, from simulateOnePos.cpp:32: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: 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:72:7: warning: 'simulateOnePos::_simulateNullModel' will be initialized after [-Wreorder] 72 | bool _simulateNullModel; | ^~~~~~~~~~~~~~~~~~ simulateOnePos.h:63:6: 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 | ^~~~~~~~~~~~~~ In file included from simulateOnePos.cpp:18: simulateOnePos.h:65:10: warning: 'simulateOnePos::_theta' will be initialized after [-Wreorder] 65 | MDOUBLE _theta; | ^~~~~~ simulateOnePos.h:64:10: 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 | ^~~~~~~~~~~~~~ In file included from simulateOnePos.cpp:18: simulateOnePos.h:75:11: warning: 'simulateOnePos::_freq_cpN' will be initialized after [-Wreorder] 75 | Vdouble* _freq_cpN; | ^~~~~~~~~ simulateOnePos.h:69:11: 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:181:9: warning: unused variable 'isRevers' [-Wunused-variable] 181 | bool isRevers = false; | ^~~~~~~~ simulateOnePos.cpp:202:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] 202 | MDOUBLE sumQii = 1.0; | ^~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp In file included from bblLS.cpp:17: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:17: 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:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:11: 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:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:11: 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:36:14: 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:112:14: warning: NULL used in arithmetic [-Wpointer-arith] 112 | if (curL == NULL) | ^~~~ g++ -g -O2 -fdebug-prefix-map=/build/fastml-3.11=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp gainLoss.cpp: In member function 'void gainLoss::startStochasticProcess()': gainLoss.cpp:869:23: warning: 'rateDist' may be used uninitialized in this function [-Wmaybe-uninitialized] 869 | if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted | ^~~~~~~~ In file included from sankoffReconstructGL.cpp:17: sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)': sankoffReconstructGL.h:85:9: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] 85 | string _outDir; | ^~~~~~~ sankoffReconstructGL.h:84:10: 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): | ^~~~~~~~~~~~~~~~~~~~ In file included from sankoffReconstructGL.cpp:17: sankoffReconstructGL.h:84:10: warning: 'sankoffReconstructGL::_costMatrixGainLossRatio' will be initialized after [-Wreorder] 84 | MDOUBLE _costMatrixGainLossRatio; | ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h:83:10: 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): | ^~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::startStochasticProcessVec()': gainLoss.cpp:1127:25: warning: 'rateDist' may be used uninitialized in this function [-Wmaybe-uninitialized] 1127 | if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted | ^~~~~~~~ mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': mainbb.cpp:428:101: warning: 'bm' may be used uninitialized in this function [-Wmaybe-uninitialized] 428 | bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); | ^ ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o ar: creating libfastml.a a - fastml.o a - bbAlg.o a - bbComputeDownAlg.o a - bbComputeUpAlg.o a - bbEvaluateSpecificAV.o a - bbfindBestAVDynProg.o a - bbNodeOrderAlg.o a - bb_options.o a - bbReport.o a - computeMarginalReconstruction.o a - jointNoGamma.o a - mainbb.o a - sequenceDataDiff.o a - suffStatComponentJointNoGamma.o ranlib libfastml.a g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml gainLoss.cpp: In member function 'void gainLoss::computeCoEvolutionScoresBasedOnSimulatedData(sequenceContainer&)': gainLoss.cpp:2511:22: warning: 'countsGL' may be used uninitialized in this function [-Wmaybe-uninitialized] 2511 | if(countsGL) delete countsGL; | ^~~~~~~~ make[3]: Leaving directory '/build/fastml-3.11/programs/fastml' gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': gainLoss.cpp:1195:10: warning: 'pDm' may be used uninitialized in this function [-Wmaybe-uninitialized] 1195 | delete pDm; | ^~~ computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': computeCorrelations.cpp:505:5: warning: 'expextedFreq' may be used uninitialized in this function [-Wmaybe-uninitialized] 505 | if(freqOfHighCorr>expextedFreq && freqOfHighCorr splitMap_test.out.tmp ./doubleRep > doubleRep.out.tmp diff splitMap_test.out.tmp splitMap_test.out.standard diff doubleRep.out.tmp doubleRep.out.standard ./split_test > split_test.out.tmp diff split_test.out.tmp split_test.out.standard ./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard ./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard ./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard ./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard ./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp diff readTreeWithComments.out.tmp readTreeWithComments.out.standard make[4]: Leaving directory '/build/fastml-3.11/libs/phylogeny/tests' make[3]: Leaving directory '/build/fastml-3.11/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.11/libs' echo test test make[1]: Leaving directory '/build/fastml-3.11' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j8 install DESTDIR=/build/fastml-3.11/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/fastml-3.11' cd libs;make all make[2]: Entering directory '/build/fastml-3.11/libs' cd phylogeny && make all make[3]: Entering directory '/build/fastml-3.11/libs/phylogeny' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/fastml-3.11/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.11/libs' cd programs;make install make[2]: Entering directory '/build/fastml-3.11/programs' cd fastml && make install cd gainLoss && make install cd indelCoder && make install make[3]: Entering directory '/build/fastml-3.11/programs/indelCoder' mkdir -p ../../bin cp indelCoder ../../bin/indelCoder make[3]: Entering directory '/build/fastml-3.11/programs/fastml' mkdir -p ../../bin cp fastml ../../bin/fastml make[3]: Entering directory '/build/fastml-3.11/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss make[3]: Leaving directory '/build/fastml-3.11/programs/indelCoder' make[3]: Leaving directory '/build/fastml-3.11/programs/fastml' make[3]: Leaving directory '/build/fastml-3.11/programs/gainLoss' make[2]: Leaving directory '/build/fastml-3.11/programs' make[1]: Leaving directory '/build/fastml-3.11' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'fastml' in '../fastml_3.11-3_arm64.deb'. dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.11-3_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../fastml_3.11-3_arm64.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/27344 and its subdirectories I: Current time: Fri Sep 16 16:39:41 -12 2022 I: pbuilder-time-stamp: 1663389581