Tue Mar 30 21:54:13 UTC 2021 I: starting to build fastml/buster/amd64 on jenkins on '2021-03-30 21:54' Tue Mar 30 21:54:13 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_14/5421/console.log Tue Mar 30 21:54:13 UTC 2021 I: Downloading source for buster/fastml=3.1-4 --2021-03-30 21:54:14-- http://deb.debian.org/debian/pool/main/f/fastml/fastml_3.1-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1888 (1.8K) Saving to: ‘fastml_3.1-4.dsc’ 0K . 100% 166M=0s 2021-03-30 21:54:14 (166 MB/s) - ‘fastml_3.1-4.dsc’ saved [1888/1888] Tue Mar 30 21:54:14 UTC 2021 I: fastml_3.1-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: fastml Binary: fastml Architecture: any Version: 3.1-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://fastml.tau.ac.il/ Standards-Version: 4.1.5 Vcs-Browser: https://salsa.debian.org/med-team/fastml Vcs-Git: https://salsa.debian.org/med-team/fastml.git Build-Depends: debhelper (>= 11~) Package-List: fastml deb science optional arch=any Checksums-Sha1: 9cbb702f60bcc6514ceb0b0155ea9c4378fe91bf 835771 fastml_3.1.orig.tar.gz d471528dc55dfdd04b0c96409ea0ace1c9345381 10080 fastml_3.1-4.debian.tar.xz Checksums-Sha256: 16c8631a4186f434f81f5b7e8c1147660e79b025b3c93a6db9889c30477bd5f4 835771 fastml_3.1.orig.tar.gz 2a8c603e40e619507c8fb94ac576eb1e2ca5a4dd924ef0a71bcde90eca7ba371 10080 fastml_3.1-4.debian.tar.xz Files: a553572d6bd96bd308e8aeea32f59f89 835771 fastml_3.1.orig.tar.gz 680887a46782b4e4d109a1a592937608 10080 fastml_3.1-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAltGWsURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtETYg/8CWUGQNtbt3HMEL1/SCA59Lc2DkH6idhc eaOrbgKSBVds/84xLLqqT9JBEhI3fY8xbyl38W9G9P87KCJiXnPKksiyb9fwK6GL CGTkkCPmZiyOPEPnHhGSzzDWeyljjXbleYN8DEhQo5YyR2xJv1BMSxLYP88yzh8X 71vlTIuneTUCWSLYKTJobz6TwjHP46WPl98JDWm5zCOOOFinowUJX5Eokw8zFK6l mK7dzS/eYwcA/EmiksbOFSw8AgrZG8zyb+HjqrpLHtOJ2VmsefMUOxNPWb+TLnfr dEU/kBjMkj/i61W7XoLDDn/7Q0Fa4DpOYSRHyx/26ZLBiYkevcIuWj2PmBC0Jjoc ssM5czTlo8OrWKBLdlqu3GdBf8fZ+VKUFFa/R+MTbv+LlUWyd4N4XirT7pKtmGys TzDoKX5VGqDpwqsi3pLUqrUgPF8EM+cwNxTri4pTCx6WCQd5CSjTQC4XvSDKjKTT YPvYQ6n8k0Ynf3XoHLvJqlbgXzm2c6DnjlYa1zsGYyElvRdJKVpD3rOjisjhDh4o zlVar6PZLyA+Y+hzG2wRyTa3dVHEkR6/eQndOsezjGLPitgQr/V5Nd9zf7pgE17J EXr7fvRlfiC5Dk5xL1FQAHcelXndXjZ4ludFMBdrhj5QpMEUvIBtmPKs72xPeLBS +eJhCYALHr8= =xAE4 -----END PGP SIGNATURE----- Tue Mar 30 21:54:14 UTC 2021 I: Checking whether the package is not for us Tue Mar 30 21:54:14 UTC 2021 I: Starting 1st build on remote node ionos5-amd64.debian.net. Tue Mar 30 21:54:14 UTC 2021 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Tue Mar 30 21:56:50 UTC 2021 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 2 16:17:20 -12 2022 I: pbuilder-time-stamp: 1651551440 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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_3.1-4.dsc] I: copying [./fastml_3.1.orig.tar.gz] I: copying [./fastml_3.1-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jul 11 07:30:13 2018 -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_3.1-4.dsc dpkg-source: info: extracting fastml in fastml-3.1 dpkg-source: info: unpacking fastml_3.1.orig.tar.gz dpkg-source: info: unpacking fastml_3.1-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc_5.patch dpkg-source: info: applying fix_makefile4test.patch dpkg-source: info: applying fix_intall_target.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying change_to_tests_dir_only_if_existing.patch dpkg-source: info: applying skip_failing_tests.patch dpkg-source: info: applying remove-template-depth.patch dpkg-source: info: applying g++-6.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/54242/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='516c9e8ed33b4e758625bb61a7fee655' 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='54242' 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.4eXPlHRDOc/pbuilderrc_cBEV --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4eXPlHRDOc/b1 --logfile b1/build.log fastml_3.1-4.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 5.10.0-0.bpo.3-amd64 #1 SMP Debian 5.10.13-1~bpo10+1 (2021-02-11) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Apr 23 02:46 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/54242/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: amd64 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 (>= 11~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 (>= 11~); however: Package debhelper 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{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 libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 19.0 MB of archives. After unpacking 69.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u2 [1258 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u1 [689 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Fetched 19.0 MB in 0s (59.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../11-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... 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Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/fastml-3.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/fastml-3.1' dh_auto_clean make -j16 clean make[2]: Entering directory '/build/fastml-3.1' cd libs;make clean cd programs;make clean make[3]: Entering directory '/build/fastml-3.1/libs' cd phylogeny && make clean make[3]: Entering directory '/build/fastml-3.1/programs' cd fastml && make clean cd gainLoss && make clean cd indelCoder && make clean make[4]: Entering directory '/build/fastml-3.1/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Entering directory '/build/fastml-3.1/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Entering directory '/build/fastml-3.1/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Leaving directory '/build/fastml-3.1/programs/fastml' make[4]: Entering directory '/build/fastml-3.1/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Leaving directory '/build/fastml-3.1/programs/indelCoder' make[4]: Leaving directory '/build/fastml-3.1/libs/phylogeny' make[3]: Leaving directory '/build/fastml-3.1/libs' make[4]: Leaving directory '/build/fastml-3.1/programs/gainLoss' make[3]: Leaving directory '/build/fastml-3.1/programs' make[2]: Leaving directory '/build/fastml-3.1' rm -f libs/phylogeny/make.dep \ programs/fastml/make.dep \ programs/gainLoss/make.dep \ programs/indelCoder/make.dep make[1]: Leaving directory '/build/fastml-3.1' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j16 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/fastml-3.1' cd libs;make all make[2]: Entering directory '/build/fastml-3.1/libs' cd phylogeny && make all make[3]: Entering directory '/build/fastml-3.1/libs/phylogeny' making depend g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o AddLog.o AddLog.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiProp.o NNiProp.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiSep.o NNiSep.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Nni.o Nni.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o aaJC.o aaJC.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTrees.o allTrees.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o alphabet.o alphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o amino.o amino.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlpha.o bestAlpha.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp bestAlphaManyTrees.cpp: In function 'void bestAlpha::optimizeAlphaNG_EM_PROP_n_alpha(tree&, std::vector&, std::vector&, const std::vector*>*, std::vector&, double&, int, double)': bestAlphaManyTrees.cpp:184:10: warning: variable 'ax' set but not used [-Wunused-but-set-variable] 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] 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] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha ^~ bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)': bestAlpha.cpp:371:10: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] MDOUBLE oldA=0; ^~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o clustalFormat.o clustalFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeCounts.o computeCounts.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeDownAlg.o computeDownAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeMarginalAlg.o computeMarginalAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlg.o computeUpAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp In file included from computeSubstitutionCounts.cpp:1: computeSubstitutionCounts.h: In constructor 'computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer&, const tree&, multipleStochasticProcess*, std::__cxx11::string&, VVVdouble&, int, double, bool)': computeSubstitutionCounts.h:57:12: warning: 'computeSubstitutionCounts::_LpostPerSpPerCat' will be initialized after [-Wreorder] VVVdouble _LpostPerSpPerCat; // _LpostPerSpPerCat[sp][rateCat][pos] ^~~~~~~~~~~~~~~~~ computeSubstitutionCounts.h:53:6: warning: 'int computeSubstitutionCounts::_simulationsIterNum' [-Wreorder] int _simulationsIterNum; ^~~~~~~~~~~~~~~~~~~ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 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] MDOUBLE _probCutOffSum; ^~~~~~~~~~~~~~ computeSubstitutionCounts.h:52:7: warning: 'bool computeSubstitutionCounts::_isSilent' [-Wreorder] bool _isSilent; ^~~~~~~~~ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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] const int _nodeID; ^~~~~~~ fromCountTableComponentToDistancePropEB.h:28:27: warning: 'const gammaDistribution* fromCountTableComponentToDistancePropEB::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^~~~~~~~~~~~~~~~ fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)': goldmanYangModel.cpp:8:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] 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] goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): ^~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.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] MDOUBLE oldIntervalSize = currentIntervalSize; ^~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o molphyFormat.o molphyFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] //* for (i=1;i&, VVdouble&, njConstraint&)': nj.cpp:122:13: warning: 'minCol' may be used uninitialized in this function [-Wmaybe-uninitialized] int minRaw,minCol; ^~~~~~ nj.cpp:133:36: warning: 'minRaw' may be used uninitialized in this function [-Wmaybe-uninitialized] UpdateDistanceTableAndCurrentNodes(currentNodes,distanceTable,nodeI,nodeJ,theNewNode,minRaw,minCol); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequenceContainer.cpp: In member function 'void sequenceContainer::removeGapPositions()': sequenceContainer.cpp:187:7: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] 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] bool gapCol; ^~~~~~ sequenceContainer.cpp: In member function 'int sequenceContainer::getNumOfOccurancesPerPos(int, char)': sequenceContainer.cpp:452:12: warning: unused variable 'len' [-Wunused-variable] 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] const int len = _seqDataVec[0].seqLen(); ^~~ sequence.cpp: In constructor 'sequence::sequence(const sequence&, const alphabet*)': sequence.cpp:76:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses] || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nj.cpp: In member function 'void NJalg::NJiterate(tree&, std::vector&, VVdouble&)': nj.cpp:100:41: warning: 'minCol' may be used uninitialized in this function [-Wmaybe-uninitialized] tree::nodeP nodeJ = currentNodes[minCol]; ^ nj.cpp:99:41: warning: 'minRaw' may be used uninitialized in this function [-Wmaybe-uninitialized] tree::nodeP nodeI = currentNodes[minRaw]; ^ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp tree.cpp: In constructor 'tree::tree(const string&)': tree.cpp:180:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 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' create_names_to_internal_nodes(); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treeUtil.cpp: In function 'std::vector getNexusTreesFromFile(const string&)': treeUtil.cpp:371:25: warning: variable 'itStrStart' set but not used [-Wunused-but-set-variable] string::const_iterator itStrStart = it->begin(); ^~~~~~~~~~ treeUtil.cpp:372:25: warning: variable 'itStrEnd' set but not used [-Wunused-but-set-variable] string::const_iterator itStrEnd = it->end(); ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.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] stochasticProcess& _sp; ^~~ bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^~~~~~~~~~~~~~~~ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] C_evalGTRParamProportional( const GTRParam param, ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistribution.o betaDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.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] vector _boundary; ^~~~~~~~~ betaDistribution.h:47:10: warning: 'double betaDistribution::_alpha' [-Wreorder] MDOUBLE _alpha; ^~~~~~ betaDistribution.cpp:23:1: warning: when initialized here [-Wreorder] betaDistribution::betaDistribution(const betaDistribution& other) : ^~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o extremeValDistribution.o extremeValDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeJumps.o computeJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.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] MDOUBLE _Lambda2; ^~~~~~~~ computeJumps.h:57:11: warning: 'double computeJumps::gFunc::_r' [-Wreorder] MDOUBLE _r; ^~ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)': seqeuncesFilter.cpp:141:18: warning: unused variable 'pAlph' [-Wunused-variable] const alphabet* pAlph = sc.getAlphabet(); ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp suffStatGammaMixture.cpp: In member function 'void suffStatGammaMixture::computeStatistics()': suffStatGammaMixture.cpp:123:12: warning: variable 'Exp_Rk' set but not used [-Wunused-but-set-variable] MDOUBLE Exp_Rk, Exp_LogRk, sum; ^~~~~~ suffStatGammaMixture.cpp: In member function 'double suffStatGammaMixture::computeQ()': suffStatGammaMixture.cpp:224:11: warning: unused variable 'first' [-Wunused-variable] MDOUBLE first = _MkVec[comp] * log(P_k); ^~~~~ suffStatGammaMixture.cpp:225:11: warning: unused variable 'second' [-Wunused-variable] MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k); ^~~~~~ suffStatGammaMixture.cpp:226:11: warning: unused variable 'third' [-Wunused-variable] MDOUBLE third = -_MkVec[comp] * gammln(alpha_k); ^~~~~ suffStatGammaMixture.cpp:227:11: warning: unused variable 'fourth' [-Wunused-variable] MDOUBLE fourth = -_AkVec[comp]*beta_k; ^~~~~~ suffStatGammaMixture.cpp:228:11: warning: unused variable 'fifth' [-Wunused-variable] MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0); ^~~~~ suffStatGammaMixture.cpp:216:10: warning: variable 'res2' set but not used [-Wunused-but-set-variable] MDOUBLE res2 = 0.0; ^~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp mixtureDistribution.cpp: In member function 'virtual const double mixtureDistribution::rates(int) const': mixtureDistribution.cpp:210:6: warning: 'componentNum' may be used uninitialized in this function [-Wmaybe-uninitialized] int componentNum, categoryInComponent, totalCat = 0; ^~~~~~~~~~~~ mixtureDistribution.cpp:221:41: warning: 'categoryInComponent' may be used uninitialized in this function [-Wmaybe-uninitialized] return _components[componentNum]->rates(categoryInComponent) * _globalRate; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp: In member function 'virtual const double mixtureDistribution::ratesProb(int) const': mixtureDistribution.cpp:228:6: warning: 'componentNum' may be used uninitialized in this function [-Wmaybe-uninitialized] int componentNum, categoryInComponent, totalCat = 0; ^~~~~~~~~~~~ In file included from mixtureDistribution.h:12, from mixtureDistribution.cpp:1: generalGammaDistribution.h:28:73: warning: 'categoryInComponent' may be used uninitialized in this function [-Wmaybe-uninitialized] virtual const MDOUBLE ratesProb(const int i) const {return _ratesProb[i];} ^ mixtureDistribution.cpp:228:20: note: 'categoryInComponent' was declared here int componentNum, categoryInComponent, totalCat = 0; ^~~~~~~~~~~~~~~~~~~ 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] 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] 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 seqeuncesFilter.h:6, from seqeuncesFilter.cpp:1: sequenceContainer.h: In static member function 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const string&, std::__cxx11::string)': sequenceContainer.h:31:81: warning: 'refID' may be used uninitialized in this function [-Wmaybe-uninitialized] const sequence& operator[](const int id) const {return _seqDataVec[_id2place[id]];} ^ seqeuncesFilter.cpp:165:6: note: 'refID' was declared here int refID; ^~~~~ 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] 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] MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2codon.o bblEM2codon.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndK.o bestAlphaAndK.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gtrModel.o gtrModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestGtrModelParams.o bestGtrModelParams.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o integerAlphabet.o integerAlphabet.cpp In file included from gtrModel.cpp:1: gtrModel.h: In constructor 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)': gtrModel.h:54:10: warning: 'gtrModel::_g2t' will be initialized after [-Wreorder] MDOUBLE _g2t; ^~~~ gtrModel.h:47:10: warning: 'Vdouble gtrModel::_freq' [-Wreorder] Vdouble _freq; ^~~~~ gtrModel.cpp:5:1: warning: when initialized here [-Wreorder] 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] stochasticProcess& _sp; ^~~ bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^~~~~~~~~~~~~~~~ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] C_evalGTRParamProportional( const GTRParam param, ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 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] 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] 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] 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] 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] 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-3.1/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.1/libs' cd programs;make all make[2]: Entering directory '/build/fastml-3.1/programs' cd fastml && make all cd gainLoss && make all cd indelCoder && make all make[3]: Entering directory '/build/fastml-3.1/programs/fastml' making depend make[3]: Entering directory '/build/fastml-3.1/programs/gainLoss' make[3]: Entering directory '/build/fastml-3.1/programs/indelCoder' making depend making depend g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoder.o indelCoder.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o character.o character.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': indelCoder.cpp:422:6: warning: unused variable 'gapNum' [-Wunused-variable] int gapNum = 1; ^~~~~~ indelCoder.cpp: In member function 'void indelCoder::printIndelSummary()': indelCoder.cpp:587:7: warning: unused variable 'isSIC' [-Wunused-variable] bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; ^~~~~ indelCoder.cpp:597:6: warning: unused variable 'seqLeng' [-Wunused-variable] int seqLeng = _sc.seqLen(); ^~~~~~~ character.cpp: In member function 'int character::getLongestGapStIndex()': character.cpp:28:9: warning: 'longestGapStIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] return longestGapStIndex; ^~~~~~~~~~~~~~~~~ character.cpp: In member function 'void character::checkForTriangleInequality(int, int)': character.cpp:6:63: warning: 'longestGapStIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][longestGapStIndex]){ ^ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.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] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.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] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ 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] const sequenceContainer& _sc; ^~~ bbEvaluateSpecificAV.h:31:23: warning: 'const computePijGam& bbEvaluateSpecificAV::_bbcpij' [-Wreorder] const computePijGam& _bbcpij; ^~~~~~~ bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] 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] MDOUBLE rate = _sp.rates(categor); // the r. ^~~~ 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] string reportFile; ^~~~~~~~~~ bb_options.h:44:9: warning: 'std::__cxx11::string bb_options::outFile_seq_joint' [-Wreorder] string outFile_seq_joint; ^~~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 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] string outFile_seq_marginal; ^~~~~~~~~~~~~~~~~~~~ bb_options.h:42:9: warning: 'std::__cxx11::string bb_options::outFile_prob_joint' [-Wreorder] string outFile_prob_joint; ^~~~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 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] string outFile_prob_marginal; ^~~~~~~~~~~~~~~~~~~~~ bb_options.h:24:9: warning: 'std::__cxx11::string bb_options::seqfile' [-Wreorder] string seqfile; ^~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 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] distributionsNames distributionName; ^~~~~~~~~~~~~~~~ bb_options.h:26:16: warning: 'bb_options::SeqFileFormat bb_options::seqOutputFormat' [-Wreorder] SeqFileFormat seqOutputFormat; ^~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 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] string outTreeFileAncestor; ^~~~~~~~~~~~~~~~~~~ bb_options.h:32:15: warning: 'bb_options::boundMethods bb_options::boundMethod' [-Wreorder] boundMethods boundMethod; ^~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 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] MDOUBLE gammaPar; ^~~~~~~~ bb_options.h:28:7: warning: 'bool bb_options::userProvideAlpha' [-Wreorder] bool userProvideAlpha; ^~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 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] int gammaCategies; ^~~~~~~~~~~~~ bb_options.h:36:19: warning: 'bb_options::modelNameOptions bb_options::modelName' [-Wreorder] modelNameOptions modelName; ^~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 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] bool useChebyshev; ^~~~~~~~~~~~ bb_options.h:27:9: warning: 'std::__cxx11::string bb_options::treeOutFile' [-Wreorder] string treeOutFile; ^~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^~~~~~~~~~ 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] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ In file included from mainbb.h:4, from fastml.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ 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] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ 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] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 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] const sequenceContainer& _sc; ^~~ bbNodeOrderAlg.h:32:23: warning: 'const computePijGam& bbNodeOrderAlg::_cpij' [-Wreorder] const computePijGam& _cpij; ^~~~~ bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, ^~~~~~~~~~~~~~ bbReport.h: In constructor 'BandBReport::BandBReport(const string&, int, int)': bbReport.h:53:16: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbReport.h:51:12: warning: 'const int BandBReport::_position' [-Wreorder] const int _position; ^~~~~~~~~ bbReport.cpp:10:1: warning: when initialized here [-Wreorder] BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : ^~~~~~~~~~~ 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] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ 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] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbAlg.h:60:20: warning: 'BandBReportAllPos bbAlg::BandBReportAllPos1' [-Wreorder] BandBReportAllPos BandBReportAllPos1; // report for all positions. ^~~~~~~~~~~~~~~~~~ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] bbAlg::bbAlg(const tree& et, ^~~~~ In file included from bbAlg.cpp:1: bbAlg.h:60:20: warning: 'bbAlg::BandBReportAllPos1' will be initialized after [-Wreorder] BandBReportAllPos BandBReportAllPos1; // report for all positions. ^~~~~~~~~~~~~~~~~~ bbAlg.h:29:14: warning: 'const tree& bbAlg::_et' [-Wreorder] const tree& _et; ^~~ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] bbAlg::bbAlg(const tree& et, ^~~~~ computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': computeMarginalReconstruction.cpp:67:11: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] MDOUBLE likelihoodOfPos = 0; ^~~~~~~~~~~~~~~ computeMarginalReconstruction.cpp:45:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] MDOUBLE totalLikelihoodOfReconstruction = 0; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': jointNoGamma.cpp:23:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] 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] MDOUBLE maxL = VERYSMALL; ^~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 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] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ 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] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp In file included from 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] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ In file included from mainbb.cpp:31: ../../libs/phylogeny/bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': ../../libs/phylogeny/bestGtrModelParams.h:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] stochasticProcess& _sp; ^~~ ../../libs/phylogeny/bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^~~~~~~~~~~~~~~~ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] C_evalGTRParamProportional( const GTRParam param, ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 -ffile-prefix-map=/build/fastml-3.1=. -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 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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] if(probs) ^ gainLossUtils.cpp:88:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if(probs) ^ 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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] Vdouble* _weightsUniqPatterns; ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.h:86:20: warning: 'unObservableData* optimizeGainLossModel::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, ^~~~~~~~~~~~~~~~~~~~~ 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] MDOUBLE normFactor; ^~~~~~~~~~ gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': gainLossUtils.cpp:788:10: warning: unused variable 'scale' [-Wunused-variable] MDOUBLE scale; ^~~~~ optimizeGainLossModel.cpp:85:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] MDOUBLE sumPijQij; ^~~~~~~~~ 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from mainbb.h:4, from mainbb.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ 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] MDOUBLE curL =NULL); ^~~~ bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 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] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:96:11: warning: when initialized here [-Wreorder] 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] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:152:11: warning: when initialized here [-Wreorder] 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] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ gainLoss.h:240:16: warning: 'distribution* gainLoss::_lossDist' [-Wreorder] distribution* _lossDist; ^~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] 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] distribution* _lossDist; ^~~~~~~~~ gainLoss.h:239:16: warning: 'distribution* gainLoss::_gainDist' [-Wreorder] distribution* _gainDist; ^~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] 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] sequence* _refSeq; // the reference sequence ^~~~~~~ gainLoss.h:267:11: warning: 'Vdouble* gainLoss::_weightsUniqPatterns' [-Wreorder] Vdouble* _weightsUniqPatterns; ^~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^~~~~~~~ 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)': gainLoss.cpp:604:7: warning: unused variable 'missigDataChar' [-Wunused-variable] char missigDataChar = -2; ^~~~~~~~~~~~~~ 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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] MDOUBLE _gain; // _Q[0][1] ^~~~~ gainLossModel.h:105:10: warning: 'Vdouble gainLossModel::_freq' [-Wreorder] Vdouble _freq; ^~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] 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] bool _isRootFreqEQstationary; ^~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:111:7: warning: 'bool gainLossModel::_isReversible' [-Wreorder] bool _isReversible; ^~~~~~~~~~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] 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] bool _isHGT_with_Q; ^~~~~~~~~~~~~ gainLossModel.h:110:8: warning: 'q2pt* gainLossModel::_q2pt' [-Wreorder] q2pt *_q2pt; // dont use q2p ^~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): ^~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': gainLoss.cpp:1245:57: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ ^~ gainLoss.cpp:1245:38: note: add parentheses around left hand side expression to silence this warning if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ ^~~~~~~~~~~~~~~~~~~ ( ) g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': gainLoss.cpp:1868:11: warning: unused variable 'sumPijQij' [-Wunused-variable] 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] MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); ^~~~~~~~~ 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'double gainLoss::computeDistanceFromRootForRecent(tree&)': gainLoss.cpp:4205:7: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] 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] 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] if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ ^ gainLoss.cpp:4382:7: note: add parentheses around left hand side expression to silence this warning if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ ^~~~~~~~~~~ ( ) 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] Vdouble* _weightsUniqPatterns; ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.h:81:20: warning: 'unObservableData* optimizeGainLossModelVV::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, ^~~~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.cpp:258:13: warning: unused variable 'currentlogL' [-Wunused-variable] 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] MDOUBLE sumPijQij; ^~~~~~~~~ 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] MDOUBLE sumQii = 1.0; ^~~~~~ 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] while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp In file included from gainLoss.h: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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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 'double getRateBeta(distribution*)': gainLossUtils.cpp:312:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] return res; ^~~ 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] MDOUBLE curL =NULL); ^~~~ bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 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] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:96:11: warning: when initialized here [-Wreorder] 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] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:152:11: warning: when initialized here [-Wreorder] 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] tree _tr; ^~~ gainLossOptimizer.h:109:21: warning: 'stochasticProcess* gainLossOptimizer::_sp' [-Wreorder] stochasticProcess *_sp; ^~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 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] sequenceContainer _sc; ^~~ gainLossOptimizer.h:93:10: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] MDOUBLE _epsilonOptimization; ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 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] Vdouble* _weightsUniqPatterns; ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:21: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 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] distribution* _lossDist; ^~~~~~~~~ gainLossOptimizer.h:135:20: warning: 'sequenceContainer gainLossOptimizer::_sc' [-Wreorder] sequenceContainer _sc; ^~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 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] sequenceContainer _sc; ^~~ gainLossOptimizer.h:93:10: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] MDOUBLE _epsilonOptimization; ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 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] Vdouble* _weightsUniqPatterns; ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:21: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:543:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp gainLossOptimizer.cpp:487:10: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengthsvv(int)': gainLossOptimizer.cpp:634:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:677:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] 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] MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 -ffile-prefix-map=/build/fastml-3.1=. -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 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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::__cxx11::string&, unObservableData*)': rate4siteGL.h:59:7: warning: 'rate4siteGL::_tr' will be initialized after [-Wreorder] tree _tr; ^~~ rate4siteGL.h:58:21: warning: 'stochasticProcess* rate4siteGL::_sp' [-Wreorder] stochasticProcess *_sp; ^~~ rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder] 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] int precisionHigh = 5; ^~~~~~~~~~~~~ rate4siteGL.cpp:152:6: warning: unused variable 'precisionLow' [-Wunused-variable] int precisionLow = 3; ^~~~~~~~~~~~ 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o ar: creating libindelCoder.a In file included from computeCountsGL.cpp:17: computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::__cxx11::string&, VVdouble&, double, bool)': computeCountsGL.h:104:7: warning: 'computeCountsGL::_tr' will be initialized after [-Wreorder] tree _tr; ^~~ computeCountsGL.h:102:21: warning: 'stochasticProcess* computeCountsGL::_sp' [-Wreorder] stochasticProcess *_sp; ^~~ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] 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] MDOUBLE _distanceFromNearestOTUForRecent; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:7: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] bool _isSilent; ^~~~~~~~~ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] 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::__cxx11::string&, VVVdouble&, double, bool)': computeCountsGL.h:109:16: warning: 'computeCountsGL::_lossDist' will be initialized after [-Wreorder] distribution* _lossDist; ^~~~~~~~~ computeCountsGL.h:105:20: warning: 'sequenceContainer computeCountsGL::_sc' [-Wreorder] sequenceContainer _sc; ^~~ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] 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] MDOUBLE _distanceFromNearestOTUForRecent; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:7: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] bool _isSilent; ^~~~~~~~~ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): ^~~~~~~~~~~~~~~ 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 indelCoder.o libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder In file included from gainLoss4site.cpp:17: gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::__cxx11::string&, unObservableData*, double)': gainLoss4site.h:68:7: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] tree _tr; ^~~ gainLoss4site.h:61:38: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] vector > _spVVec; //save stochasticProcess for each category ^~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 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] unObservableData* _unObservableData_p; // ^~~~~~~~~~~~~~~~~~~ gainLoss4site.h:78:10: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] MDOUBLE _alphaConf; ^~~~~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 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] 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] int isHigherNminReducedFreqOfHighCorr = false; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:348:7: warning: unused variable 'typeIndex' [-Wunused-variable] 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] if(!simCorrelStream==NULL) ^~~~ computeCorrelations.cpp:569:24: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp computeCorrelations.cpp:579:24: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^~~~ computeCorrelations.cpp:584:23: warning: NULL used in arithmetic [-Wpointer-arith] 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] int prevNumberOfSimulationsInRange = 1; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:677:9: warning: variable 'prevNumberOfSimulationPointsMoreExtremeOrEqToCorr' set but not used [-Wunused-but-set-variable] int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:679:9: warning: unused variable 'numOfBinsWithLowerSignificance' [-Wunused-variable] 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] 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] if(!numOfSites_A == numOfSites_B){ ^~ computeCorrelations.cpp:894:5: note: add parentheses around left hand side expression to silence this warning if(!numOfSites_A == numOfSites_B){ ^~~~~~~~~~~~~ ( ) 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] 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] return returnType; ^~~~~~~~~~ computeCorrelations.cpp: In member function 'void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::__cxx11::string*)': computeCorrelations.cpp:1009:7: warning: unused variable 'isPearson' [-Wunused-variable] bool isPearson = false; ^~~~~~~~~ computeCorrelations.cpp:1025:6: warning: unused variable 'numOfbranches' [-Wunused-variable] 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:1347:112: warning: narrowing conversion of 'gainLossOptions::_pValueCutOffForBootStrap' from 'double' to 'float' inside { } [-Wnarrowing] 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] it_B it_siteB = it_siteA->second.begin(); ^~~~~~~~ make[3]: Leaving directory '/build/fastml-3.1/programs/indelCoder' g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': mainbb.cpp:428:101: warning: 'bm' may be used uninitialized in this function [-Wmaybe-uninitialized] bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); ^ 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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 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] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 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::__cxx11::string, std::ostream*, std::ostream*, int, std::__cxx11::string, double, double, bool, stochasticProcess*, tree*, Vdouble*, Vdouble*)': simulateOnePos.h:72:7: warning: 'simulateOnePos::_simulateNullModel' will be initialized after [-Wreorder] bool _simulateNullModel; ^~~~~~~~~~~~~~~~~~ simulateOnePos.h:63:6: warning: 'int simulateOnePos::_simNum' [-Wreorder] int _simNum; ^~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 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] MDOUBLE _theta; ^~~~~~ simulateOnePos.h:64:10: warning: 'double simulateOnePos::_sumGainLoss' [-Wreorder] MDOUBLE _sumGainLoss; ^~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 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] Vdouble* _freq_cpN; ^~~~~~~~~ simulateOnePos.h:69:11: warning: 'std::ostream* simulateOnePos::_simulatedEvents' [-Wreorder] ostream *_simulatedEvents; ^~~~~~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile ^~~~~~~~~~~~~~ simulateOnePos.cpp: In member function 'void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::__cxx11::string)': simulateOnePos.cpp:181:9: warning: unused variable 'isRevers' [-Wunused-variable] bool isRevers = false; ^~~~~~~~ simulateOnePos.cpp:202:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] MDOUBLE sumQii = 1.0; ^~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': gainLossOptimizer.cpp:833:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] return res; ^~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp In file included from bblLS.cpp:17: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^~~~ bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] 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] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:96:11: warning: when initialized here [-Wreorder] 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] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:152:11: warning: when initialized here [-Wreorder] 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] 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] if (curL == NULL) ^~~~ In file included from sankoffReconstructGL.cpp:17: sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::__cxx11::string&, double, double)': sankoffReconstructGL.h:85:9: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] string _outDir; ^~~~~~~ sankoffReconstructGL.h:84:10: warning: 'double sankoffReconstructGL::_costMatrixGainLossRatio' [-Wreorder] MDOUBLE _costMatrixGainLossRatio; ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 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] MDOUBLE _costMatrixGainLossRatio; ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h:83:10: warning: 'double sankoffReconstructGL::_distanceFromRootForRecent' [-Wreorder] MDOUBLE _distanceFromRootForRecent; ^~~~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): ^~~~~~~~~~~~~~~~~~~~ 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 fastml.o libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml gainLoss.cpp: In 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] if(probInvariant) updateLossProbInvariant(bestLossProbInvariant,lossDist); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/fastml-3.1/programs/fastml' In file included from gainLoss.h:35, from gainLoss.cpp:20: gainLossModel.h: In function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': gainLossModel.h:173:14: warning: 'currM2' may be used uninitialized in this function [-Wmaybe-uninitialized] _Q[1][1] = -_loss; ^~~~~~ gainLoss.cpp:1842:10: note: 'currM2' was declared here MDOUBLE currM2; ^~~~~~ In file included from gainLoss.h:35, from gainLoss.cpp:20: gainLossModel.h: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': gainLossModel.h:173:14: warning: 'currM2' may be used uninitialized in this function [-Wmaybe-uninitialized] _Q[1][1] = -_loss; ^~~~~~ gainLoss.cpp:1842:10: note: 'currM2' was declared here MDOUBLE currM2; ^~~~~~ 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] if(probInvariant) updateLossProbInvariant(bestLossProbInvariant,lossDist); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] return returnType; ^~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()': gainLoss.cpp:3980:52: warning: 'AlphaLoss' may be used uninitialized in this function [-Wmaybe-uninitialized] gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); ~~~~~~~~~~^~~~~~~~~~~ gainLoss.cpp:3980:52: warning: 'AlphaGain' may be used uninitialized in this function [-Wmaybe-uninitialized] 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] if(freqOfHighCorr>expextedFreq && freqOfHighCorr doubleRep.out.tmp diff doubleRep.out.tmp doubleRep.out.standard ./split_test > split_test.out.tmp diff split_test.out.tmp split_test.out.standard ./splitMap_test > splitMap_test.out.tmp diff splitMap_test.out.tmp splitMap_test.out.standard ./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp diff readTreeWithComments.out.tmp readTreeWithComments.out.standard ./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard ./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.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 ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard make[4]: Leaving directory '/build/fastml-3.1/libs/phylogeny/tests' make[3]: Leaving directory '/build/fastml-3.1/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.1/libs' echo test test make[1]: Leaving directory '/build/fastml-3.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j16 install DESTDIR=/build/fastml-3.1/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/fastml-3.1' cd libs;make all make[2]: Entering directory '/build/fastml-3.1/libs' cd phylogeny && make all make[3]: Entering directory '/build/fastml-3.1/libs/phylogeny' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/fastml-3.1/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.1/libs' cd programs;make install make[2]: Entering directory '/build/fastml-3.1/programs' cd fastml && make install cd gainLoss && make install cd indelCoder && make install make[3]: Entering directory '/build/fastml-3.1/programs/indelCoder' mkdir -p ../../bin cp indelCoder ../../bin/indelCoder make[3]: Entering directory '/build/fastml-3.1/programs/fastml' mkdir -p ../../bin cp fastml ../../bin/fastml make[3]: Entering directory '/build/fastml-3.1/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss make[3]: Leaving directory '/build/fastml-3.1/programs/indelCoder' make[3]: Leaving directory '/build/fastml-3.1/programs/fastml' make[3]: Leaving directory '/build/fastml-3.1/programs/gainLoss' make[2]: Leaving directory '/build/fastml-3.1/programs' make[1]: Leaving directory '/build/fastml-3.1' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'fastml' in '../fastml_3.1-4_amd64.deb'. dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.1-4_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../fastml_3.1-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/54242 and its subdirectories I: Current time: Mon May 2 16:19:54 -12 2022 I: pbuilder-time-stamp: 1651551594 Tue Mar 30 21:56:51 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Tue Mar 30 21:56:51 UTC 2021 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Tue Mar 30 22:00:02 UTC 2021 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Tue Mar 30 22:00:02 UTC 2021 I: fastml_3.1-4_amd64.changes: Format: 1.8 Date: Wed, 11 Jul 2018 21:21:03 +0200 Source: fastml Binary: fastml fastml-dbgsym Architecture: amd64 Version: 3.1-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: fastml - maximum likelihood ancestral amino-acid sequence reconstruction Changes: fastml (3.1-4) unstable; urgency=medium . * Cleanup d/rules * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.5 Checksums-Sha1: 53c6b83f7cb36bbd6734f4b0f8e3d2ab568c9b06 23805736 fastml-dbgsym_3.1-4_amd64.deb 0c9797fb2e63938f3d89bcc0a44c35b7655ea6f9 4631 fastml_3.1-4_amd64.buildinfo 804b1b8ca0d69848ea07d9d852131543a6074e81 953280 fastml_3.1-4_amd64.deb Checksums-Sha256: c50d0ee6bbc2d44f77cb461c3b0c62448c4668fc5363097b5487605bb2adfd3f 23805736 fastml-dbgsym_3.1-4_amd64.deb 18d3f9276e95cb2d082415573fc40592683901bd3f4233c3c6cfe8b7dc3596bc 4631 fastml_3.1-4_amd64.buildinfo ef7c4cc062f099f27ce02da84b7e58a550e435c2b59b92ba41f2c33db0237c14 953280 fastml_3.1-4_amd64.deb Files: f8c4e2d0ff9174d61083bc4797268079 23805736 debug optional fastml-dbgsym_3.1-4_amd64.deb df5e057dbf9ee9e700adeef727fa2eee 4631 science optional fastml_3.1-4_amd64.buildinfo 425489701a108fa761bebdc5ebe698cf 953280 science optional fastml_3.1-4_amd64.deb Tue Mar 30 22:00:04 UTC 2021 I: diffoscope 170 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.4eXPlHRDOc/fastml_3.1-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.4eXPlHRDOc/fastml_3.1-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.4eXPlHRDOc/fastml_3.1-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.4eXPlHRDOc/b1/fastml_3.1-4_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.4eXPlHRDOc/b2/fastml_3.1-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 2.117s) 2.117s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.289s) 0.289s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Mar 30 22:00:08 UTC 2021 I: diffoscope 170 found no differences in the changes files, and a .buildinfo file also exists. Tue Mar 30 22:00:08 UTC 2021 I: fastml from buster built successfully and reproducibly on amd64. Tue Mar 30 22:00:09 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Mar 30 22:00:09 UTC 2021 I: Submitting 8.0K b1/fastml_3.1-4_amd64.buildinfo.asc Tue Mar 30 22:00:10 UTC 2021 I: Submitting 8.0K b2/fastml_3.1-4_amd64.buildinfo.asc Tue Mar 30 22:00:11 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Mar 30 22:00:11 UTC 2021 I: Done submitting .buildinfo files. Tue Mar 30 22:00:11 UTC 2021 I: Removing signed fastml_3.1-4_amd64.buildinfo.asc files: removed './b1/fastml_3.1-4_amd64.buildinfo.asc' removed './b2/fastml_3.1-4_amd64.buildinfo.asc'