Thu Jul 16 18:06:08 UTC 2020 I: starting to build phast/buster/armhf on jenkins on '2020-07-16 18:05' Thu Jul 16 18:06:08 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_35/1847/console.log Thu Jul 16 18:06:08 UTC 2020 I: Downloading source for buster/phast=1.4+dfsg-1 --2020-07-16 18:06:08-- http://deb.debian.org/debian/pool/main/p/phast/phast_1.4+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2007 (2.0K) Saving to: ‘phast_1.4+dfsg-1.dsc’ 0K . 100% 224M=0s 2020-07-16 18:06:08 (224 MB/s) - ‘phast_1.4+dfsg-1.dsc’ saved [2007/2007] Thu Jul 16 18:06:08 UTC 2020 I: phast_1.4+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: phast Binary: phast Architecture: any Version: 1.4+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://compgen.cshl/edu/phast Standards-Version: 4.1.0 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/phast.git Vcs-Git: https://anonscm.debian.org/git/debian-med/phast.git Build-Depends: debhelper (>= 10), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man Package-List: phast deb science optional arch=any Checksums-Sha1: 477417c682ae6160244b28597091a85ea9f4cd95 1808112 phast_1.4+dfsg.orig.tar.xz 45dcd2d7e2baf6074bfed173f86c2f11485125d8 51488 phast_1.4+dfsg-1.debian.tar.xz Checksums-Sha256: 3019c4177d06a7fd157efe7d1d462260de871ccd1b781c00cbe350dbf9e8f04b 1808112 phast_1.4+dfsg.orig.tar.xz 8837f5ad719cc801c1741c47a78829bab162c645a90505eabc2d3ecc89888548 51488 phast_1.4+dfsg-1.debian.tar.xz Files: 26afa32046a88663da46f82a6db7a46f 1808112 phast_1.4+dfsg.orig.tar.xz 270176e048a4eff69823e13943ca57b8 51488 phast_1.4+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAln/mjQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHpOg/9Fyxb0k3i+V5zFaTnNmCI0tT+qgWRZ2px IQTFLgDT0O551hvaYymgM3oiEtkY2hc0Yu5fFjSxJXF1toYplI+qqzsZGi1Ixokj nI6fX+gyAM1DM/Fe/aarjJaW3WIHRYLWjfwDII2cTWO181poeMWEGFWbNkyjyPER vZ5Vf4vtouYsaWYJsL+kLQDevfwGmjtZWRhKip0sLewt7d0ZsUIRXvMstz6XDPha ZXwyXxTB9y1AjHKYEv4Gl4V+N5/IRflIduVktup+oD7uVdWn47Vwdl5OlGrBfPRA nZaPenYGdcakDkkccxhH16w6Lc5YR/g/iahFyjLkVT+7jJYvIJPCJm8b8/vYlaZX zAONJOAPe5lWwOinNBagcDPkT9ZB4CmH7zKVmP6gIwhDLTj5SE+sANrDaTO4vc2B 9jRq5aaXEwgj9mQ3vR74phN9/KrP1tQUCvKfk8gMMKJDnbSnkCKKd4H8rOixi1gs Uknmhi/zQoA1ltg3CPr/SXJrfqyLFf9gYWTA7sq3K0ycKdCANDCpCMtMZRGzMHXe f2q2aNJvAMWlQxa1iJ/T7xtRuqdoZjnbSanKydzXOSE/tFjm9iMJVXxuXh1E9Odi ZqTKu5CymP0a7By+LUBuc7M4OvxlAxXxu2KprfeuafPDcbQlwK65Ygg+brolGM6o OWpY/frLpLc= =zt8h -----END PGP SIGNATURE----- Thu Jul 16 18:06:08 UTC 2020 I: Checking whether the package is not for us Thu Jul 16 18:06:08 UTC 2020 I: Starting 1st build on remote node p64b-armhf-rb.debian.net. Thu Jul 16 18:06:08 UTC 2020 I: Preparing to do remote build '1' on p64b-armhf-rb.debian.net. Thu Jul 16 18:48:05 UTC 2020 I: Deleting $TMPDIR on p64b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 16 06:06:38 -12 2020 I: pbuilder-time-stamp: 1594922798 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [phast_1.4+dfsg-1.dsc] I: copying [./phast_1.4+dfsg.orig.tar.xz] I: copying [./phast_1.4+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Nov 5 11:09:40 2017 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./phast_1.4+dfsg-1.dsc dpkg-source: info: extracting phast in phast-1.4+dfsg dpkg-source: info: unpacking phast_1.4+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.4+dfsg-1.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/24265/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='286c79dcc7a74143826ac67cfb9342ff' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='24265' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.DZ8b6JhxB0/pbuilderrc_7pG1 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.DZ8b6JhxB0/b1 --logfile b1/build.log phast_1.4+dfsg-1.dsc' SUDO_GID='115' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux p64b 4.19.0-9-arm64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 15 21:16 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/24265/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 10), 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 ... 18932 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 (>= 10); however: Package debhelper 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libicu63{a} liblapack-dev{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpcre16-3{a} libpcre3-dev{a} libpcre32-3{a} libpcrecpp0v5{a} libpipeline1{a} libsigsegv2{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 libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 46 newly installed, 0 to remove and 0 not upgraded. Need to get 23.6 MB of archives. After unpacking 79.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf liblocale-gettext-perl armhf 1.07-3+b4 [18.4 kB] Get: 8 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 10 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 11 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 12 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 14 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 16 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 17 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 18 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 20 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 23 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 25 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 31 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 32 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 34 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 35 http://deb.debian.org/debian buster/main armhf help2man armhf 1.47.8 [176 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libblas3 armhf 3.8.0-2 [109 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libblas-dev armhf 3.8.0-2 [117 kB] Get: 39 http://deb.debian.org/debian buster/main armhf liblapack3 armhf 3.8.0-2 [1631 kB] Get: 40 http://deb.debian.org/debian buster/main armhf liblapack-dev armhf 3.8.0-2 [1680 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libpcre16-3 armhf 2:8.39-12 [238 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libpcre32-3 armhf 2:8.39-12 [231 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libpcrecpp0v5 armhf 2:8.39-12 [150 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libpcre3-dev armhf 2:8.39-12 [585 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libtmglib3 armhf 3.8.0-2 [97.2 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libtmglib-dev armhf 3.8.0-2 [100 kB] Fetched 23.6 MB in 15s (1594 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../06-liblocale-gettext-perl_1.07-3+b4_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../07-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../09-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../12-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... 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Preparing to unpack .../39-liblapack-dev_3.8.0-2_armhf.deb ... Unpacking liblapack-dev:armhf (3.8.0-2) ... Selecting previously unselected package libpcre16-3:armhf. Preparing to unpack .../40-libpcre16-3_2%3a8.39-12_armhf.deb ... Unpacking libpcre16-3:armhf (2:8.39-12) ... Selecting previously unselected package libpcre32-3:armhf. Preparing to unpack .../41-libpcre32-3_2%3a8.39-12_armhf.deb ... Unpacking libpcre32-3:armhf (2:8.39-12) ... Selecting previously unselected package libpcrecpp0v5:armhf. Preparing to unpack .../42-libpcrecpp0v5_2%3a8.39-12_armhf.deb ... Unpacking libpcrecpp0v5:armhf (2:8.39-12) ... Selecting previously unselected package libpcre3-dev:armhf. Preparing to unpack .../43-libpcre3-dev_2%3a8.39-12_armhf.deb ... Unpacking libpcre3-dev:armhf (2:8.39-12) ... Selecting previously unselected package libtmglib3:armhf. Preparing to unpack .../44-libtmglib3_3.8.0-2_armhf.deb ... Unpacking libtmglib3:armhf (3.8.0-2) ... Selecting previously unselected package libtmglib-dev:armhf. Preparing to unpack .../45-libtmglib-dev_3.8.0-2_armhf.deb ... Unpacking libtmglib-dev:armhf (3.8.0-2) ... Setting up libpcrecpp0v5:armhf (2:8.39-12) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up libpcre16-3:armhf (2:8.39-12) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libpcre32-3:armhf (2:8.39-12) ... Setting up autopoint (0.19.8.1-9) ... Setting up libgfortran5:armhf (8.3.0-6) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up libpcre3-dev:armhf (2:8.39-12) ... Setting up m4 (1.4.18-2) ... Setting up help2man (1.47.8) ... Setting up libblas3:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libblas-dev:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up liblapack3:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libtmglib3:armhf (3.8.0-2) ... Setting up liblapack-dev:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up libtmglib-dev:armhf (3.8.0-2) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/phast-1.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.4+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/phast-1.4+dfsg' dh_auto_clean cd src && make clean make[2]: Entering directory '/build/phast-1.4+dfsg/src' make[3]: Entering directory '/build/phast-1.4+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-1.4+dfsg/src/lib/$dir && make clean ; done make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/base' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/msa' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/feature' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/motif' rm -f *.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/motif' rm -f /build/phast-1.4+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/phast-1.4+dfsg/src/lib' make[3]: Entering directory '/build/phast-1.4+dfsg/src/dless' rm -f *.o dless.help dlessP.help /build/phast-1.4+dfsg/src/dless/../../bin/dless /build/phast-1.4+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/phast-1.4+dfsg/src/dless' make[3]: Entering directory '/build/phast-1.4+dfsg/src/exoniphy' rm -f *.o *.help /build/phast-1.4+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/phast-1.4+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastCons' rm -f *.o /build/phast-1.4+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastOdds' rm -f *.o *.help /build/phast-1.4+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastMotif' rm -f *.o /build/phast-1.4+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloFit' rm -f *.o /build/phast-1.4+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloBoot' rm -f *.o *.help /build/phast-1.4+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloP' rm -f *.o /build/phast-1.4+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/phast-1.4+dfsg/src/phyloP' make[3]: Entering directory '/build/phast-1.4+dfsg/src/prequel' rm -f *.o /build/phast-1.4+dfsg/src/prequel/../../bin/pbsDecode /build/phast-1.4+dfsg/src/prequel/../../bin/pbsEncode /build/phast-1.4+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/phast-1.4+dfsg/src/prequel/../../bin/pbsTrain /build/phast-1.4+dfsg/src/prequel/../../bin/prequel pbsTrain.help pbsDecode.help pbsEncode.help prequel.help pbsScoreMatrix.help make[3]: Leaving directory '/build/phast-1.4+dfsg/src/prequel' make[3]: Entering directory '/build/phast-1.4+dfsg/src/util' rm -f *.o *.help /build/phast-1.4+dfsg/src/util/../../bin/hmm_train /build/phast-1.4+dfsg/src/util/../../bin/hmm_tweak /build/phast-1.4+dfsg/src/util/../../bin/stringiphy /build/phast-1.4+dfsg/src/util/../../bin/indelHistory /build/phast-1.4+dfsg/src/util/../../bin/clean_genes /build/phast-1.4+dfsg/src/util/../../bin/treeGen /build/phast-1.4+dfsg/src/util/../../bin/base_evolve /build/phast-1.4+dfsg/src/util/../../bin/all_dists /build/phast-1.4+dfsg/src/util/../../bin/tree_doctor /build/phast-1.4+dfsg/src/util/../../bin/msa_diff /build/phast-1.4+dfsg/src/util/../../bin/indelFit /build/phast-1.4+dfsg/src/util/../../bin/consEntropy /build/phast-1.4+dfsg/src/util/../../bin/convert_coords /build/phast-1.4+dfsg/src/util/../../bin/hmm_view /build/phast-1.4+dfsg/src/util/../../bin/phast /build/phast-1.4+dfsg/src/util/../../bin/maf_parse /build/phast-1.4+dfsg/src/util/../../bin/msa_split /build/phast-1.4+dfsg/src/util/../../bin/modFreqs /build/phast-1.4+dfsg/src/util/../../bin/eval_predictions /build/phast-1.4+dfsg/src/util/../../bin/chooseLines /build/phast-1.4+dfsg/src/util/../../bin/display_rate_matrix /build/phast-1.4+dfsg/src/util/../../bin/draw_tree /build/phast-1.4+dfsg/src/util/../../bin/makeHKY /build/phast-1.4+dfsg/src/util/../../bin/phastBias /build/phast-1.4+dfsg/src/util/../../bin/refeature /build/phast-1.4+dfsg/src/util/../../bin/msa_view make[3]: Leaving directory '/build/phast-1.4+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/phast-1.4+dfsg/src' make[1]: Leaving directory '/build/phast-1.4+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j3 make[1]: Entering directory '/build/phast-1.4+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-1.4+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-1.4+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/phast-1.4+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/phast-1.4+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/base' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar: creating /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/msa' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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] int i, start_idx, length, max_tuples, block_no, ^~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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] int maxlen, i, nseqs, j, do_toupper, line_no; ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /build/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/msa' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/feature' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 ar rs /build/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /build/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /build/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /build/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /build/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/feature' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/hmm' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o ar rs /build/phast-1.4+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/hmm' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/phylo' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); ^~~~~~~~~~~ ~~~~~~~~~~~ bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] sprintf(warning_str, "%s)\n", warning_str); ^~~~~~~~~~~ ~~~~~~~~~~~ bgc_hmm.c:241:31: warning: ', ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 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 sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgc_hmm.c:242:29: warning: ') ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 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 sprintf(warning_str, "%s)\n", warning_str); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/phylo' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/phylo_hmm' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 ar rs /build/phast-1.4+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phylo_hmm.o gap_patterns.o ar rs /build/phast-1.4+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phylo_hmm.o gap_patterns.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/motif' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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] int i, nseqs, j, do_toupper, line_no; ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 ar rs /build/phast-1.4+dfsg/src/lib/motif/../../../lib/libphast.a tfbs.o motif.o ar rs /build/phast-1.4+dfsg/src/lib/motif/../../../lib/libphast.a tfbs.o motif.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/motif' make[3]: Leaving directory '/build/phast-1.4+dfsg/src/lib' make[3]: Entering directory '/build/phast-1.4+dfsg/src/dless' ../munge-help.sh dless.help_src > dless.help ../munge-help.sh dlessP.help_src > dlessP.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/dless/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/dless/../../lib -o /build/phast-1.4+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-1.4+dfsg/src/dless' make[3]: Entering directory '/build/phast-1.4+dfsg/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/exoniphy/../../lib -o /build/phast-1.4+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-1.4+dfsg/src/exoniphy' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/phastCons/../../lib -o /build/phast-1.4+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-1.4+dfsg/src/phastCons' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/phastOdds/../../lib -o /build/phast-1.4+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-1.4+dfsg/src/phastOdds' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phastMotif' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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] int i, j, separate_backgd = 0, ^~~~~~~~~~~~~~~ gcc -L/build/phast-1.4+dfsg/src/phastMotif/../../lib -o /build/phast-1.4+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-1.4+dfsg/src/phastMotif' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/phyloFit/../../lib -o /build/phast-1.4+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-1.4+dfsg/src/phyloFit' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/phyloBoot/../../lib -o /build/phast-1.4+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-1.4+dfsg/src/phyloBoot' make[3]: Entering directory '/build/phast-1.4+dfsg/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/phyloP/../../lib -o /build/phast-1.4+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-1.4+dfsg/src/phyloP' make[3]: Entering directory '/build/phast-1.4+dfsg/src/prequel' ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh prequel.help_src > prequel.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/prequel/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/prequel/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/prequel/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/prequel/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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 gcc -L/build/phast-1.4+dfsg/src/prequel/../../lib -o /build/phast-1.4+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-1.4+dfsg/src/prequel' make[3]: Entering directory '/build/phast-1.4+dfsg/src/util' ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh treeGen.help_src > treeGen.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh consEntropy.help_src > consEntropy.help gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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] char tuple_i[mod->order+2], tuple_j[mod->order+2]; ^~~~~~~ gcc -L/build/phast-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+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 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+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-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+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-1.4+dfsg/src' make[1]: Leaving directory '/build/phast-1.4+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j3 install DESTDIR=/build/phast-1.4\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/phast-1.4+dfsg' (cd src; make install DESTDIR=/build/phast-1.4+dfsg/debian/phast ) make[2]: Entering directory '/build/phast-1.4+dfsg/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p /build/phast-1.4+dfsg/debian/phast/usr/bin/ mkdir -p /build/phast-1.4+dfsg/debian/phast/usr/share/phast/data/ mkdir -p /build/phast-1.4+dfsg/debian/phast/usr/share/man/man1/ cp ../bin/* /build/phast-1.4+dfsg/debian/phast/usr/bin/ cp -R ../data/* /build/phast-1.4+dfsg/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /build/phast-1.4+dfsg/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/build/phast-1.4+dfsg/src' make[1]: Leaving directory '/build/phast-1.4+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/phastOdds debian/phast/usr/bin/base_evolve debian/phast/usr/bin/refeature debian/phast/usr/bin/hmm_view debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/msa_diff debian/phast/usr/bin/convert_coords debian/phast/usr/bin/phyloFit debian/phast/usr/bin/makeHKY debian/phast/usr/bin/draw_tree debian/phast/usr/bin/modFreqs debian/phast/usr/bin/treeGen debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/chooseLines debian/phast/usr/bin/clean_genes debian/phast/usr/bin/phastMotif debian/phast/usr/bin/dlessP debian/phast/usr/bin/stringiphy debian/phast/usr/bin/phastCons debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/msa_view debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/phyloP debian/phast/usr/bin/dless debian/phast/usr/bin/consEntropy debian/phast/usr/bin/indelHistory debian/phast/usr/bin/prequel debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/exoniphy debian/phast/usr/bin/phast debian/phast/usr/bin/indelFit debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/phastBias debian/phast/usr/bin/msa_split debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/all_dists debian/phast/usr/bin/maf_parse debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/hmm_train were not linked against libtmglib.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/phastOdds debian/phast/usr/bin/base_evolve debian/phast/usr/bin/refeature debian/phast/usr/bin/hmm_view debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/msa_diff debian/phast/usr/bin/convert_coords debian/phast/usr/bin/phyloFit debian/phast/usr/bin/makeHKY debian/phast/usr/bin/draw_tree debian/phast/usr/bin/modFreqs debian/phast/usr/bin/treeGen debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/chooseLines debian/phast/usr/bin/clean_genes debian/phast/usr/bin/phastMotif debian/phast/usr/bin/dlessP debian/phast/usr/bin/stringiphy debian/phast/usr/bin/phastCons debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/msa_view debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/phyloP debian/phast/usr/bin/dless debian/phast/usr/bin/consEntropy debian/phast/usr/bin/indelHistory debian/phast/usr/bin/prequel debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/exoniphy debian/phast/usr/bin/phast debian/phast/usr/bin/indelFit debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/phastBias debian/phast/usr/bin/msa_split debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/all_dists debian/phast/usr/bin/maf_parse debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/hmm_train were not linked against libblas.so.3 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phast' in '../phast_1.4+dfsg-1_armhf.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.4+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../phast_1.4+dfsg-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/24265 and its subdirectories I: Current time: Thu Jul 16 06:46:50 -12 2020 I: pbuilder-time-stamp: 1594925210 Thu Jul 16 18:48:08 UTC 2020 I: 1st build successful. Starting 2nd build on remote node ff2a-armhf-rb.debian.net. Thu Jul 16 18:48:08 UTC 2020 I: Preparing to do remote build '2' on ff2a-armhf-rb.debian.net. Thu Jul 16 18:54:01 UTC 2020 I: Deleting $TMPDIR on ff2a-armhf-rb.debian.net. Thu Jul 16 18:54:04 UTC 2020 I: phast_1.4+dfsg-1_armhf.changes: Format: 1.8 Date: Tue, 12 Sep 2017 10:11:38 +0200 Source: phast Binary: phast phast-dbgsym Architecture: armhf Version: 1.4+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: phast - phylogenetic analysis with space/time models Closes: 875555 Changes: phast (1.4+dfsg-1) unstable; urgency=medium . * Initial release (Closes: #875555) Checksums-Sha1: ba52cec3d8586ce0c2333bec13e7a305ea8c2417 31371292 phast-dbgsym_1.4+dfsg-1_armhf.deb b0b019ab99b046ca4105d4c9fd1e892c8468226f 4850 phast_1.4+dfsg-1_armhf.buildinfo c5125dd313f288f2fa21961c10a0b66ae91f5105 1312852 phast_1.4+dfsg-1_armhf.deb Checksums-Sha256: d41d53048d000b130a4126be23ce440208ac2d06c39201ef4662a79dc5f5cb37 31371292 phast-dbgsym_1.4+dfsg-1_armhf.deb 4afef1650ca179ae7e06b13db57e77d85c2fdca40c3d05666d2a47fa064a86a4 4850 phast_1.4+dfsg-1_armhf.buildinfo 3fc3fee97d5d81ac791247016401cd8dd22f7845143d999b96f379e85e651e58 1312852 phast_1.4+dfsg-1_armhf.deb Files: 4c33dee10ebcfc8c71e6c5d9135ddf23 31371292 debug optional phast-dbgsym_1.4+dfsg-1_armhf.deb 052d5544e88f82cd221f08b0355487da 4850 science optional phast_1.4+dfsg-1_armhf.buildinfo 8684c474115f8d9b5c253367a3460a86 1312852 science optional phast_1.4+dfsg-1_armhf.deb Thu Jul 16 18:54:17 UTC 2020 I: diffoscope 151 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.DZ8b6JhxB0/phast_1.4+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.DZ8b6JhxB0/phast_1.4+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.DZ8b6JhxB0/phast_1.4+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.DZ8b6JhxB0/b1/phast_1.4+dfsg-1_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.DZ8b6JhxB0/b2/phast_1.4+dfsg-1_armhf.changes ## close_archive (total time: 0.008s) 0.004s 80 calls diffoscope.comparators.deb.DebTarContainer 0.003s 92 calls diffoscope.comparators.xz.XzContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer ## command (total time: 2320.062s) 669.354s 1935 calls diff 558.703s 2816 calls objdump 471.500s 17862 calls readelf 338.928s 76 calls objcopy 277.193s 92 calls xz 3.137s 440 calls strings 1.245s 47 calls cmp 0.001s 13 calls cmp (internal) ## compare_files (cumulative) (total time: 6977.916s) 1261.487s 1 call abc.DotChangesFile 1260.717s 2 calls abc.DebFile 1259.320s 4 calls abc.XzFile 1250.684s 2 calls abc.DebDataTarFile 1243.008s 40 calls abc.ElfFile 624.929s 160 calls diffoscope.comparators.elf.ElfCodeSection 70.854s 574 calls diffoscope.comparators.elf.ElfSection 4.658s 38 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 1.120s 4 calls diffoscope.comparators.elf.ElfStringSection 0.713s 2 calls abc.TarFile 0.363s 2 calls abc.Md5sumsFile 0.064s 1 call abc.TextFile ## container_extract (total time: 313.039s) 277.242s 92 calls diffoscope.comparators.xz.XzContainer 33.335s 486 calls diffoscope.comparators.deb.DebTarContainer 2.451s 96 calls diffoscope.comparators.deb.DebContainer 0.011s 16 calls diffoscope.comparators.tar.TarContainer ## has_same_content_as (total time: 1.274s) 1.066s 40 calls abc.ElfFile 0.076s 4 calls abc.XzFile 0.068s 2 calls abc.DebFile 0.049s 2 calls abc.DebDataTarFile 0.010s 574 calls diffoscope.comparators.elf.ElfSection 0.002s 160 calls diffoscope.comparators.elf.ElfCodeSection 0.001s 4 calls abc.TextFile 0.001s 38 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.001s 4 calls abc.Md5sumsFile 0.001s 2 calls abc.TarFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 4 calls diffoscope.comparators.elf.ElfStringSection ## main (total time: 1412.603s) 1409.228s 2 calls outputs 3.375s 1 call cleanup ## open_archive (total time: 0.004s) 0.002s 92 calls diffoscope.comparators.xz.XzContainer 0.001s 80 calls diffoscope.comparators.deb.DebTarContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer ## output (total time: 145.222s) 103.055s 1 call html 33.028s 1 call text 9.139s 1 call json ## recognizes (total time: 319.277s) 272.212s 1344 calls diffoscope.comparators.utils.archive.ArchiveMember 39.421s 8900 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 5.034s 10332 calls diffoscope.comparators.elf.ElfSection 1.265s 2880 calls diffoscope.comparators.elf.ElfCodeSection 1.027s 10 calls diffoscope.comparators.binary.FilesystemFile 0.177s 684 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.074s 72 calls diffoscope.comparators.elf.ElfStringSection 0.065s 168 calls diffoscope.comparators.debian.DebControlMember 0.000s 8 calls abc.DotChangesFile 0.000s 28 calls abc.Md5sumsFile 0.000s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink Thu Jul 16 20:01:28 UTC 2020 E: phast failed to build reproducibly in buster on armhf. Thu Jul 16 20:05:08 UTC 2020 I: Submitting .buildinfo files to external archives: Thu Jul 16 20:05:08 UTC 2020 I: Submitting 8.0K b1/phast_1.4+dfsg-1_armhf.buildinfo.asc Thu Jul 16 20:05:10 UTC 2020 I: Submitting 8.0K b2/phast_1.4+dfsg-1_armhf.buildinfo.asc Thu Jul 16 20:05:11 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jul 16 20:05:11 UTC 2020 I: Done submitting .buildinfo files. Thu Jul 16 20:05:11 UTC 2020 I: Removing signed phast_1.4+dfsg-1_armhf.buildinfo.asc files: removed './b1/phast_1.4+dfsg-1_armhf.buildinfo.asc' removed './b2/phast_1.4+dfsg-1_armhf.buildinfo.asc'