Wed Jun 24 19:02:33 UTC 2020 I: starting to build phast/buster/i386 on jenkins on '2020-06-24 19:02' Wed Jun 24 19:02:33 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_6/1934/console.log Wed Jun 24 19:02:33 UTC 2020 I: Downloading source for buster/phast=1.4+dfsg-1 --2020-06-24 19:02:33-- 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% 163M=0s 2020-06-24 19:02:33 (163 MB/s) - ‘phast_1.4+dfsg-1.dsc’ saved [2007/2007] Wed Jun 24 19:02:33 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----- Wed Jun 24 19:02:33 UTC 2020 I: Checking whether the package is not for us Wed Jun 24 19:02:33 UTC 2020 I: Starting 1st build on remote node profitbricks-build6-i386.debian.net. Wed Jun 24 19:02:33 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build6-i386.debian.net. Wed Jun 24 19:04:09 UTC 2020 I: Deleting $TMPDIR on profitbricks-build6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jul 27 13:25:32 -12 2021 I: pbuilder-time-stamp: 1627435532 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: using eatmydata during job 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/39985/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='fb7f307c216048d4b319a86fd02634bd' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='39985' 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.UmwjovkSYn/pbuilderrc_69DY --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.UmwjovkSYn/b1 --logfile b1/build.log phast_1.4+dfsg-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux profitbricks-build6-i386 4.19.0-9-amd64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 17768 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 38692 Feb 28 2019 cat -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash -rwxr-xr-x 1 root root 120676 Feb 28 2019 date -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd -rwxr-xr-x 1 root root 100620 Feb 28 2019 df -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir -rwxr-xr-x 1 root root 79412 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 34532 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 34532 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 206392 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 100952 Jan 5 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln -rwxr-xr-x 1 root root 55400 Jul 26 2018 login -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 9 2019 more -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 157832 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 38660 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 27 02:47 sh -> dash -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty -rwsr-xr-x 1 root root 71072 Jan 9 2019 su -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch -rwxr-xr-x 1 root root 34532 Feb 28 2019 true -rwxr-xr-x 1 root root 17768 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34208 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/39985/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: i386 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 ... 19234 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 26.0 MB of archives. After unpacking 96.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 liblocale-gettext-perl i386 1.07-3+b4 [19.3 kB] Get: 8 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 10 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 11 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 12 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 13 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 14 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 16 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 17 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 18 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 19 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 20 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 23 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 24 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 25 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 30 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 31 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 32 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 34 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 35 http://deb.debian.org/debian buster/main i386 help2man i386 1.47.8 [177 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libgfortran5 i386 8.3.0-6 [549 kB] Get: 37 http://deb.debian.org/debian buster/main i386 libblas3 i386 3.8.0-2 [142 kB] Get: 38 http://deb.debian.org/debian buster/main i386 libblas-dev i386 3.8.0-2 [150 kB] Get: 39 http://deb.debian.org/debian buster/main i386 liblapack3 i386 3.8.0-2 [1974 kB] Get: 40 http://deb.debian.org/debian buster/main i386 liblapack-dev i386 3.8.0-2 [2035 kB] Get: 41 http://deb.debian.org/debian buster/main i386 libpcre16-3 i386 2:8.39-12 [258 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libpcre32-3 i386 2:8.39-12 [250 kB] Get: 43 http://deb.debian.org/debian buster/main i386 libpcrecpp0v5 i386 2:8.39-12 [153 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libpcre3-dev i386 2:8.39-12 [656 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libtmglib3 i386 3.8.0-2 [128 kB] Get: 46 http://deb.debian.org/debian buster/main i386 libtmglib-dev i386 3.8.0-2 [132 kB] Fetched 26.0 MB in 0s (82.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.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_i386.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_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... 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Unpacking libtmglib-dev:i386 (3.8.0-2) ... Setting up libpcrecpp0v5:i386 (2:8.39-12) ... Setting up libpipeline1:i386 (1.5.1-2) ... Setting up libpcre16-3:i386 (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:i386 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:i386 (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:i386 (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up libpcre32-3:i386 (2:8.39-12) ... Setting up autopoint (0.19.8.1-9) ... Setting up libgfortran5:i386 (8.3.0-6) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libxml2:i386 (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:i386 (2:8.39-12) ... Setting up m4 (1.4.18-2) ... Setting up help2man (1.47.8) ... Setting up libblas3:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) 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:i386 (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:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) 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:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) 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:i386 (3.8.0-2) ... Setting up liblapack-dev:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode Setting up libtmglib-dev:i386 (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 i386 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/indelHistory /build/phast-1.4+dfsg/src/util/../../bin/hmm_train /build/phast-1.4+dfsg/src/util/../../bin/modFreqs /build/phast-1.4+dfsg/src/util/../../bin/draw_tree /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/msa_view /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/hmm_tweak /build/phast-1.4+dfsg/src/util/../../bin/stringiphy /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/consEntropy /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/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/all_dists /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 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 -j18 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 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 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 misc.c -o misc.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O2 -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 ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.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 eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.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 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 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 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 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 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 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 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 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 tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o tree_model.o bgc_hmm.o ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_likelihoods.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.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 prequel.c: In function 'main': prequel.c:285:32: warning: '.bin' directive writing 4 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(out_fname, "%s.%s.bin", out_root, n->name); ^~~~ prequel.c:285:7: note: 'sprintf' output 6 or more bytes (assuming 261) into a destination of size 256 sprintf(out_fname, "%s.%s.bin", out_root, n->name); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prequel.c:253:32: warning: '.fa' directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(out_fname, "%s.%s.fa", out_root, n->name); ^~~ prequel.c:253:7: note: 'sprintf' output 5 or more bytes (assuming 260) into a destination of size 256 sprintf(out_fname, "%s.%s.fa", out_root, n->name); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prequel.c:203:32: warning: '.probs' directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(out_fname, "%s.%s.probs", out_root, n->name); ^~~~~~ prequel.c:203:7: note: 'sprintf' output 8 or more bytes (assuming 263) into a destination of size 256 sprintf(out_fname, "%s.%s.probs", out_root, n->name); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 indelHistory.help_src > indelHistory.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh treeGen.help_src > treeGen.help ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh makeHKY.help_src > makeHKY.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 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 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 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 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 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 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 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 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 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 consEntropy.c -o consEntropy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition consEntropy.c: In function 'main': consEntropy.c:157:5: warning: 'new_exp_len' may be used uninitialized in this function [-Wmaybe-uninitialized] printf("Recommended expected length: omega=%f sites (for L_min*H=%f)\n", new_exp_len, LminH); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 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 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 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 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 -j18 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/modFreqs debian/phast/usr/bin/dlessP debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/msa_diff debian/phast/usr/bin/all_dists debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/indelHistory debian/phast/usr/bin/refeature debian/phast/usr/bin/consEntropy debian/phast/usr/bin/hmm_view debian/phast/usr/bin/treeGen debian/phast/usr/bin/draw_tree debian/phast/usr/bin/chooseLines debian/phast/usr/bin/phyloFit debian/phast/usr/bin/stringiphy debian/phast/usr/bin/phastBias debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/phastMotif debian/phast/usr/bin/exoniphy debian/phast/usr/bin/maf_parse debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/clean_genes debian/phast/usr/bin/hmm_train debian/phast/usr/bin/phyloP debian/phast/usr/bin/base_evolve debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/phastOdds debian/phast/usr/bin/indelFit debian/phast/usr/bin/phastCons debian/phast/usr/bin/msa_view debian/phast/usr/bin/makeHKY debian/phast/usr/bin/convert_coords debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/msa_split debian/phast/usr/bin/phast debian/phast/usr/bin/dless debian/phast/usr/bin/prequel were not linked against libblas.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/modFreqs debian/phast/usr/bin/dlessP debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/msa_diff debian/phast/usr/bin/all_dists debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/indelHistory debian/phast/usr/bin/refeature debian/phast/usr/bin/consEntropy debian/phast/usr/bin/hmm_view debian/phast/usr/bin/treeGen debian/phast/usr/bin/draw_tree debian/phast/usr/bin/chooseLines debian/phast/usr/bin/phyloFit debian/phast/usr/bin/stringiphy debian/phast/usr/bin/phastBias debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/phastMotif debian/phast/usr/bin/exoniphy debian/phast/usr/bin/maf_parse debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/clean_genes debian/phast/usr/bin/hmm_train debian/phast/usr/bin/phyloP debian/phast/usr/bin/base_evolve debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/phastOdds debian/phast/usr/bin/indelFit debian/phast/usr/bin/phastCons debian/phast/usr/bin/msa_view debian/phast/usr/bin/makeHKY debian/phast/usr/bin/convert_coords debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/msa_split debian/phast/usr/bin/phast debian/phast/usr/bin/dless debian/phast/usr/bin/prequel were not linked against libtmglib.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_i386.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.4+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../phast_1.4+dfsg-1_i386.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/39985 and its subdirectories I: Current time: Tue Jul 27 13:27:06 -12 2021 I: pbuilder-time-stamp: 1627435626 Wed Jun 24 19:04:09 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build12-i386.debian.net. Wed Jun 24 19:04:09 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build12-i386.debian.net. Wed Jun 24 19:13:42 UTC 2020 I: Deleting $TMPDIR on profitbricks-build12-i386.debian.net. Wed Jun 24 19:13:42 UTC 2020 I: phast_1.4+dfsg-1_i386.changes: Format: 1.8 Date: Tue, 12 Sep 2017 10:11:38 +0200 Source: phast Binary: phast phast-dbgsym Architecture: i386 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: c759a7111ef7307e8ac1bb3bdc5d5562ec0ff427 33304912 phast-dbgsym_1.4+dfsg-1_i386.deb fc9b86c8a462f394e26ac87646cdf70c3c63a61c 4950 phast_1.4+dfsg-1_i386.buildinfo 22e4e479833f921b72a12aaafc5f8d21e1703ca5 2362124 phast_1.4+dfsg-1_i386.deb Checksums-Sha256: 51d5f6135e69d73f9849b56a4ed597855bdd12b7f3e4965a33154ac1f0b92b09 33304912 phast-dbgsym_1.4+dfsg-1_i386.deb 9f7d80aa2a5ff204600e8f2001c5437b6893ccb72eba9581155b3fff08707ce2 4950 phast_1.4+dfsg-1_i386.buildinfo b0adf120019cea7f2d0bc22a3441b19f38ac99a07597324d04a5331048cd8df3 2362124 phast_1.4+dfsg-1_i386.deb Files: 328090119a6b39696c6f42b9e8744006 33304912 debug optional phast-dbgsym_1.4+dfsg-1_i386.deb d151652f52fbe8f01968deb3e0a1459d 4950 science optional phast_1.4+dfsg-1_i386.buildinfo 2f31f7fd49070f564391d09250e293f1 2362124 science optional phast_1.4+dfsg-1_i386.deb Wed Jun 24 19:13:44 UTC 2020 I: diffoscope 148 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.UmwjovkSYn/phast_1.4+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.UmwjovkSYn/phast_1.4+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.UmwjovkSYn/phast_1.4+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.UmwjovkSYn/b1/phast_1.4+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/tmp.UmwjovkSYn/b2/phast_1.4+dfsg-1_i386.changes ## close_archive (total time: 0.006s) 0.003s 82 calls diffoscope.comparators.deb.DebTarContainer 0.002s 94 calls diffoscope.comparators.xz.XzContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer ## command (total time: 2047.259s) 603.824s 1985 calls diff 489.956s 3795 calls objdump 414.052s 17445 calls readelf 307.059s 78 calls objcopy 225.876s 94 calls xz 4.815s 429 calls strings 1.676s 47 calls cmp 0.001s 12 calls cmp (internal) ## compare_files (cumulative) (total time: 6829.794s) 1233.390s 1 call abc.DotChangesFile 1231.910s 2 calls abc.DebFile 1229.897s 4 calls abc.XzFile 1222.307s 2 calls abc.DebDataTarFile 1214.957s 39 calls abc.ElfFile 608.633s 195 calls diffoscope.comparators.elf.ElfCodeSection 82.711s 507 calls diffoscope.comparators.elf.ElfSection 5.229s 39 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.581s 2 calls abc.TarFile 0.090s 2 calls abc.Md5sumsFile 0.087s 1 call abc.TextFile ## container_extract (total time: 240.895s) 225.893s 94 calls diffoscope.comparators.xz.XzContainer 14.395s 488 calls diffoscope.comparators.deb.DebTarContainer 0.594s 98 calls diffoscope.comparators.deb.DebContainer 0.013s 16 calls diffoscope.comparators.tar.TarContainer ## has_same_content_as (total time: 1.714s) 1.416s 39 calls abc.ElfFile 0.143s 4 calls abc.XzFile 0.071s 2 calls abc.DebFile 0.071s 2 calls abc.DebDataTarFile 0.007s 507 calls diffoscope.comparators.elf.ElfSection 0.002s 195 calls diffoscope.comparators.elf.ElfCodeSection 0.001s 4 calls abc.Md5sumsFile 0.001s 2 calls abc.TarFile 0.000s 39 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.000s 2 calls abc.TextFile 0.000s 2 calls abc.JSONFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 1 call abc.DotChangesFile ## main (total time: 1452.869s) 1451.481s 2 calls outputs 1.387s 1 call cleanup ## open_archive (total time: 0.004s) 0.002s 82 calls diffoscope.comparators.deb.DebTarContainer 0.002s 94 calls diffoscope.comparators.xz.XzContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer ## output (total time: 217.418s) 188.521s 1 call html 17.052s 1 call text 11.844s 1 call json ## recognizes (total time: 293.894s) 220.287s 1362 calls diffoscope.comparators.utils.archive.ArchiveMember 62.487s 8990 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 5.974s 9126 calls diffoscope.comparators.elf.ElfSection 2.307s 168 calls diffoscope.comparators.debian.DebControlMember 2.182s 3510 calls diffoscope.comparators.elf.ElfCodeSection 0.468s 10 calls diffoscope.comparators.binary.FilesystemFile 0.188s 702 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.000s 28 calls abc.Md5sumsFile 0.000s 8 calls abc.DotChangesFile 0.000s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink Wed Jun 24 19:38:04 UTC 2020 E: phast failed to build reproducibly in buster on i386. Wed Jun 24 19:44:24 UTC 2020 I: Submitting .buildinfo files to external archives: Wed Jun 24 19:44:24 UTC 2020 I: Submitting 8.0K b1/phast_1.4+dfsg-1_i386.buildinfo.asc Wed Jun 24 19:44:25 UTC 2020 I: Submitting 8.0K b2/phast_1.4+dfsg-1_i386.buildinfo.asc Wed Jun 24 19:44:26 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Jun 24 19:44:26 UTC 2020 I: Done submitting .buildinfo files. Wed Jun 24 19:44:26 UTC 2020 I: Removing signed phast_1.4+dfsg-1_i386.buildinfo.asc files: removed './b1/phast_1.4+dfsg-1_i386.buildinfo.asc' removed './b2/phast_1.4+dfsg-1_i386.buildinfo.asc'