I: pbuilder: network access will be disabled during build I: Current time: Wed Nov 16 09:35:23 +14 2022 I: pbuilder-time-stamp: 1668540923 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [phast_1.5+dfsg-2.dsc] I: copying [./phast_1.5+dfsg.orig.tar.xz] I: copying [./phast_1.5+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.l285umtH/trustedkeys.kbx': General error gpgv: Signature made Sat Oct 3 22:26:48 2020 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./phast_1.5+dfsg-2.dsc dpkg-source: info: extracting phast in phast-1.5+dfsg dpkg-source: info: unpacking phast_1.5+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.5+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying clapack.patch dpkg-source: info: applying do_not_install_to_opt.patch dpkg-source: info: applying use_debian_packaged_libpcre.patch dpkg-source: info: applying use_debian_packaged_help2man.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_test_makefile.patch dpkg-source: info: applying arm64.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1239618/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1239618/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1239618/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=3de226f563db4ed9b659266aeb82733a LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1239618 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.c6mfYfHqch/pbuilderrc_mVMx --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.c6mfYfHqch/b2 --logfile b2/build.log phast_1.5+dfsg-2.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jul 29 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 29 2021 more -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Nov 16 09:35 sh -> bash lrwxrwxrwx 1 root root 4 Nov 10 05:47 sh.distrib -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jul 29 2021 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 29 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/1239618/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-compat (= 13), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19655 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libtmglib-dev; however: Package libtmglib-dev is not installed. pbuilder-satisfydepends-dummy depends on libpcre3-dev; however: Package libpcre3-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu67{a} liblapack-dev{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpcre16-3{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtmglib-dev{a} libtmglib3{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 27.6 MB of archives. After unpacking 110 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 help2man amd64 1.48.1 [190 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libblas-dev amd64 3.9.0-3 [161 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 liblapack-dev amd64 3.9.0-3 [4247 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libpcre16-3 amd64 2:8.39-13 [259 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libpcre32-3 amd64 2:8.39-13 [250 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libpcrecpp0v5 amd64 2:8.39-13 [152 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libpcre3-dev amd64 2:8.39-13 [650 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libtmglib3 amd64 3.9.0-3 [134 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libtmglib-dev amd64 3.9.0-3 [135 kB] Fetched 27.6 MB in 1s (40.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19655 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../05-liblocale-gettext-perl_1.07-4+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../08-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../11-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../21-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../24-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../26-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../27-libxml2_2.9.10+dfsg-6.7_amd64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package hostname: Name or service not known I: Running cd /build/phast-1.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../phast_1.5+dfsg-2_source.changes dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.5+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/phast-1.5+dfsg' dh_auto_clean cd src && make clean make[2]: Entering directory '/build/phast-1.5+dfsg/src' make[3]: Entering directory '/build/phast-1.5+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-1.5+dfsg/src/lib/$dir && make clean ; done make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/base' rm -f *.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/msa' rm -f *.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/feature' rm -f *.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/motif' rm -f *.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/motif' rm -f /build/phast-1.5+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/phast-1.5+dfsg/src/lib' make[3]: Entering directory '/build/phast-1.5+dfsg/src/dless' rm -f *.o dless.help dlessP.help /build/phast-1.5+dfsg/src/dless/../../bin/dless /build/phast-1.5+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/phast-1.5+dfsg/src/dless' make[3]: Entering directory '/build/phast-1.5+dfsg/src/exoniphy' rm -f *.o *.help /build/phast-1.5+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/phast-1.5+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phastCons' rm -f *.o /build/phast-1.5+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phastOdds' rm -f *.o *.help /build/phast-1.5+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phastMotif' rm -f *.o /build/phast-1.5+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phyloFit' rm -f *.o /build/phast-1.5+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phyloBoot' rm -f *.o *.help /build/phast-1.5+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phyloP' rm -f *.o /build/phast-1.5+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phyloP' make[3]: Entering directory '/build/phast-1.5+dfsg/src/prequel' rm -f *.o /build/phast-1.5+dfsg/src/prequel/../../bin/pbsDecode /build/phast-1.5+dfsg/src/prequel/../../bin/pbsEncode /build/phast-1.5+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/phast-1.5+dfsg/src/prequel/../../bin/pbsTrain /build/phast-1.5+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/build/phast-1.5+dfsg/src/prequel' make[3]: Entering directory '/build/phast-1.5+dfsg/src/util' rm -f *.o *.help /build/phast-1.5+dfsg/src/util/../../bin/all_dists /build/phast-1.5+dfsg/src/util/../../bin/base_evolve /build/phast-1.5+dfsg/src/util/../../bin/chooseLines /build/phast-1.5+dfsg/src/util/../../bin/clean_genes /build/phast-1.5+dfsg/src/util/../../bin/consEntropy /build/phast-1.5+dfsg/src/util/../../bin/convert_coords /build/phast-1.5+dfsg/src/util/../../bin/display_rate_matrix /build/phast-1.5+dfsg/src/util/../../bin/draw_tree /build/phast-1.5+dfsg/src/util/../../bin/eval_predictions /build/phast-1.5+dfsg/src/util/../../bin/hmm_train /build/phast-1.5+dfsg/src/util/../../bin/hmm_tweak /build/phast-1.5+dfsg/src/util/../../bin/hmm_view /build/phast-1.5+dfsg/src/util/../../bin/indelFit /build/phast-1.5+dfsg/src/util/../../bin/indelHistory /build/phast-1.5+dfsg/src/util/../../bin/maf_parse /build/phast-1.5+dfsg/src/util/../../bin/makeHKY /build/phast-1.5+dfsg/src/util/../../bin/modFreqs /build/phast-1.5+dfsg/src/util/../../bin/msa_diff /build/phast-1.5+dfsg/src/util/../../bin/msa_split /build/phast-1.5+dfsg/src/util/../../bin/msa_view /build/phast-1.5+dfsg/src/util/../../bin/phast /build/phast-1.5+dfsg/src/util/../../bin/phastBias /build/phast-1.5+dfsg/src/util/../../bin/refeature /build/phast-1.5+dfsg/src/util/../../bin/stringiphy /build/phast-1.5+dfsg/src/util/../../bin/treeGen /build/phast-1.5+dfsg/src/util/../../bin/tree_doctor make[3]: Leaving directory '/build/phast-1.5+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/phast-1.5+dfsg/src' make[1]: Leaving directory '/build/phast-1.5+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j16 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/phast-1.5+dfsg' Type "make package" to create a tarball reflecting the current state of the CVS tree. (cd src; make DESTDIR= CLAPACKPATH=/usr/lib ) make[2]: Entering directory '/build/phast-1.5+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /build/phast-1.5+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/phast-1.5+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-1.5+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/base' gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c complex_matrix.c -o complex_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c complex_vector.c -o complex_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c eigen.c -o eigen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c hashtable.c -o hashtable.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c list_of_lists.c -o list_of_lists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c lists.c -o lists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c markov_matrix.c -o markov_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c matrix.c -o matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c memory_handler.c -o memory_handler.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c misc.c -o misc.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c numerical_opt.c -o numerical_opt.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c prob_matrix.c -o prob_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c prob_vector.c -o prob_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c stringsplus.c -o stringsplus.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c vector.c -o vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar: creating /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /build/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/msa' gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c local_alignment.c -o local_alignment.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c maf.c -o maf.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition maf.c: In function 'maf_read_cats_subset': maf.c:29:41: warning: variable 'block_no' set but not used [-Wunused-but-set-variable] 29 | int i, start_idx, length, max_tuples, block_no, | ^~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c maf_block.c -o maf_block.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c msa.c -o msa.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition msa.c: In function 'msa_read_fasta': msa.c:257:40: warning: variable 'line_no' set but not used [-Wunused-but-set-variable] 257 | int maxlen, i, nseqs, j, do_toupper, line_no; | ^~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c multi_msa.c -o multi_msa.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c sufficient_stats.c -o sufficient_stats.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition sufficient_stats.c: In function 'ss_from_msas': sufficient_stats.c:140:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 140 | else | ^~~~ sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 142 | max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1, | ^~~~~~~~~~ ar rs /build/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o ar rs /build/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o ar rs /build/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o ar rs /build/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o ar rs /build/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o ar rs /build/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/feature' gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c bed.c -o bed.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c category_map.c -o category_map.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c genepred.c -o genepred.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c gff.c -o gff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c wig.c -o wig.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /build/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /build/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /build/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /build/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /build/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/hmm' gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c em.c -o em.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c hmm.c -o hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /build/phast-1.5+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o ar rs /build/phast-1.5+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/phylo' gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c bgc_hmm.c -o bgc_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition bgc_hmm.c: In function 'bgcHmm': bgc_hmm.c:241:31: warning: ', ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 241 | sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); | ^~ bgc_hmm.c:241:7: note: 'sprintf' output 3 or more bytes (assuming 10002) into a destination of size 10000 241 | sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgc_hmm.c:241:7: warning: 'sprintf' argument 3 overlaps destination object 'warning_str' [-Wrestrict] bgc_hmm.c:235:10: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 235 | char warning_str[10000]; | ^~~~~~~~~~~ bgc_hmm.c:242:29: warning: ') ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 242 | sprintf(warning_str, "%s)\n", warning_str); | ^~~ bgc_hmm.c:242:5: note: 'sprintf' output between 3 and 10002 bytes into a destination of size 10000 242 | sprintf(warning_str, "%s)\n", warning_str); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgc_hmm.c:242:5: warning: 'sprintf' argument 3 overlaps destination object 'warning_str' [-Wrestrict] bgc_hmm.c:235:10: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 235 | char warning_str[10000]; | ^~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c dgamma.c -o dgamma.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_column.c -o fit_column.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_em.c -o fit_em.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_feature.c -o fit_feature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c indel_history.c -o indel_history.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c indel_mod.c -o indel_mod.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_fit.c -o phylo_fit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_p.c -o phylo_p.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_p_print.c -o phylo_p_print.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c subst_distrib.c -o subst_distrib.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c subst_mods.c -o subst_mods.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c tree_likelihoods.c -o tree_likelihoods.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c tree_model.c -o tree_model.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c trees.c -o trees.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /build/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/phylo_hmm' gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c gap_patterns.c -o gap_patterns.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phylo_hmm.c -o phylo_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /build/phast-1.5+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a gap_patterns.o phylo_hmm.o ar rs /build/phast-1.5+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a gap_patterns.o phylo_hmm.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-1.5+dfsg/src/lib/motif' gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c motif.c -o motif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition motif.c: In function 'mtf_print': motif.c:1411:7: warning: '%s' directive argument is null [-Wformat-overflow=] 1411 | fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ motif.c: In function 'mtf_print_html': motif.c:1604:7: warning: '%s' directive argument is null [-Wformat-overflow=] 1604 | fprintf(F, "
  • %s\n", (char*)lst_get_ptr(notfound, i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c tfbs.c -o tfbs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition tfbs.c: In function 'ms_read': tfbs.c:219:32: warning: variable 'line_no' set but not used [-Wunused-but-set-variable] 219 | int i, nseqs, j, do_toupper, line_no; | ^~~~~~~ ar rs /build/phast-1.5+dfsg/src/lib/motif/../../../lib/libphast.a motif.o tfbs.o ar rs /build/phast-1.5+dfsg/src/lib/motif/../../../lib/libphast.a motif.o tfbs.o make[4]: Leaving directory '/build/phast-1.5+dfsg/src/lib/motif' make[3]: Leaving directory '/build/phast-1.5+dfsg/src/lib' make[3]: Entering directory '/build/phast-1.5+dfsg/src/dless' ../munge-help.sh dless.help_src > dless.help ../munge-help.sh dlessP.help_src > dlessP.help gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/dless/../..\" -fno-strict-aliasing -c bd_phylo_hmm.c -o bd_phylo_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/dless/../../lib -o /build/phast-1.5+dfsg/src/dless/../../bin/dless dless.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/dless/../..\" -fno-strict-aliasing -c dlessP.c -o dlessP.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/dless/../../lib -o /build/phast-1.5+dfsg/src/dless/../../bin/dlessP dlessP.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.5+dfsg/src/dless' make[3]: Entering directory '/build/phast-1.5+dfsg/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/exoniphy/../../lib -o /build/phast-1.5+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.5+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/phastCons/../../lib -o /build/phast-1.5+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/phastOdds/../../lib -o /build/phast-1.5+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phastMotif' gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phastMotif.c: In function 'main': phastMotif.c:131:13: warning: variable 'separate_backgd' set but not used [-Wunused-but-set-variable] 131 | int i, j, separate_backgd = 0, | ^~~~~~~~~~~~~~~ gcc -L/build/phast-1.5+dfsg/src/phastMotif/../../lib -o /build/phast-1.5+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/phyloFit/../../lib -o /build/phast-1.5+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/phyloBoot/../../lib -o /build/phast-1.5+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-1.5+dfsg/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/phyloP/../../lib -o /build/phast-1.5+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.5+dfsg/src/phyloP' make[3]: Entering directory '/build/phast-1.5+dfsg/src/prequel' ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh prequel.help_src > prequel.help gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c simplex_grid.c -o simplex_grid.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbs_code.c -o pbs_code.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/prequel/../../lib -o /build/phast-1.5+dfsg/src/prequel/../../bin/pbsDecode pbsDecode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsEncode.c -o pbsEncode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/prequel/../../lib -o /build/phast-1.5+dfsg/src/prequel/../../bin/pbsEncode pbsEncode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsScoreMatrix.c -o pbsScoreMatrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/prequel/../../lib -o /build/phast-1.5+dfsg/src/prequel/../../bin/pbsScoreMatrix pbsScoreMatrix.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/prequel/../../lib -o /build/phast-1.5+dfsg/src/prequel/../../bin/pbsTrain pbsTrain.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c prequel.c -o prequel.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition prequel.c: In function 'main': prequel.c:285:32: warning: '.bin' directive writing 4 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 285 | sprintf(out_fname, "%s.%s.bin", out_root, n->name); | ^~~~ prequel.c:285:7: note: 'sprintf' output 6 or more bytes (assuming 261) into a destination of size 256 285 | sprintf(out_fname, "%s.%s.bin", out_root, n->name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prequel.c:253:32: warning: '.fa' directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 253 | sprintf(out_fname, "%s.%s.fa", out_root, n->name); | ^~~ prequel.c:253:7: note: 'sprintf' output 5 or more bytes (assuming 260) into a destination of size 256 253 | sprintf(out_fname, "%s.%s.fa", out_root, n->name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prequel.c:203:32: warning: '.probs' directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 203 | sprintf(out_fname, "%s.%s.probs", out_root, n->name); | ^~~~~~ prequel.c:203:7: note: 'sprintf' output 8 or more bytes (assuming 263) into a destination of size 256 203 | sprintf(out_fname, "%s.%s.probs", out_root, n->name); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -L/build/phast-1.5+dfsg/src/prequel/../../lib -o /build/phast-1.5+dfsg/src/prequel/../../bin/prequel prequel.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.5+dfsg/src/prequel' make[3]: Entering directory '/build/phast-1.5+dfsg/src/util' ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh consEntropy.help_src > consEntropy.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh treeGen.help_src > treeGen.help gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition display_rate_matrix.c: In function 'do_context_dependent_ti_tv': display_rate_matrix.c:204:8: warning: variable 'tuple_i' set but not used [-Wunused-but-set-variable] 204 | char tuple_i[mod->order+2], tuple_j[mod->order+2]; | ^~~~~~~ gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -fdebug-prefix-map=/build/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/build/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.5+dfsg/src/util/../../lib -o /build/phast-1.5+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.5+dfsg/src/util' mkdir -p ../doc/man/ Generating man pages... USAGE: convert_coords -m -f [-s ] [-d ] [-p] [-n] [-i PHYLIP|FASTA|MPM] DESCRIPTION: Converts coordinates of features in a GFF file according to a multiple alignment. Will map from the coordinate system of any sequence to any other sequence; can also map to or from the coordinate system of the entire alignment. In addition, supports translation of coordinates by specified offset. OPTIONS: -m (required) Name of file in which alignment is defined. -f (required) Name of file in which features are defined (GFF). -s Index of frame of reference for feature coordinates, as defined in the GFF file. Use an integer 1-N (if N seqs) or 0 to indicate the coordinate system of the alignment as a whole. Default behavior is to match features with alignment sequences by name (feature by feature). -d Index of destination frame of reference. Default is 0 (whole MSA). -p Positive coordinate offset. This value will be added to all coordinates. Useful when the alignment (or sequence) for which the coordinates are specified is a sub-alignment of yours. -n Negative coordinate offset. This value will be subtracted from all coordinates. Useful when your alignment is a sub-alignment of the alignment (or sequence) for which the coordinates are specified. -i FASTA|PHYLIP|MPM|SS Alignment format. Default is to guess format from file contents PROGRAM: draw_tree DESCRIPTION: Produces a simple postscript rendering of a tree. USAGE: draw_tree [-dbvs] | OPTIONS: (Required) File name of tree (expected to be in Newick format, unless filename ends with '.mod', in which case expected to be a tree model file). -d Print "diagonal" branches, instead of "right-angle" or "square" ones (produces a "cladogram", as opposed to a "phenogram"). This option implies -s. -b Suppress branch lengths. -v Vertical layout. -s Don't draw branches to scale. Done. make[2]: Leaving directory '/build/phast-1.5+dfsg/src' make[1]: Leaving directory '/build/phast-1.5+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/phast-1.5+dfsg' cd test && PATH=/build/phast-1.5+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path make msa_view make[2]: Entering directory '/build/phast-1.5+dfsg/test' *** Testing msa_view *** msa_view hmrc.ss -i SS --end 10000 > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o PHYLIP > hmrc.ph msa_view hmrc.ph -i PHYLIP > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm msa_view hmrc.mpm --in-format MPM > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o SS > hmrc_short_a.ss msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa msa_view --seqs human,cow hmrc.fa > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --summary -i SS > hmrc_summary if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi Passed all tests. make[2]: Leaving directory '/build/phast-1.5+dfsg/test' make[1]: Leaving directory '/build/phast-1.5+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j16 install DESTDIR=/build/phast-1.5\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/phast-1.5+dfsg' (cd src; make install DESTDIR=/build/phast-1.5+dfsg/debian/phast ) make[2]: Entering directory '/build/phast-1.5+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p /build/phast-1.5+dfsg/debian/phast/usr/bin/ mkdir -p /build/phast-1.5+dfsg/debian/phast/usr/share/phast/data/ mkdir -p /build/phast-1.5+dfsg/debian/phast/usr/share/man/man1/ cp ../bin/* /build/phast-1.5+dfsg/debian/phast/usr/bin/ cp -R ../data/* /build/phast-1.5+dfsg/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /build/phast-1.5+dfsg/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/build/phast-1.5+dfsg/src' make[1]: Leaving directory '/build/phast-1.5+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phast' in '../phast_1.5+dfsg-2_amd64.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.5+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../phast_1.5+dfsg-2_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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1239618/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1239618/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1239618 and its subdirectories I: Current time: Wed Nov 16 09:38:14 +14 2022 I: pbuilder-time-stamp: 1668541094