Diff of the two buildlogs: -- --- b1/build.log 2020-06-24 19:04:08.859162492 +0000 +++ b2/build.log 2020-06-24 19:13:41.640761908 +0000 @@ -1,6 +1,8 @@ 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: Current time: Thu Jun 25 09:04:13 +14 2020 +I: pbuilder-time-stamp: 1593025453 +I: cleaning the build env +I: removing directory /srv/workspace/pbuilder/30568 and its subdirectories I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +20,7 @@ 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: Signature made Mon Nov 6 13:09:40 2017 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -34,138 +36,172 @@ 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: user script /srv/workspace/pbuilder/30568/tmp/hooks/D01_modify_environment starting +debug: Running on profitbricks-build12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/30568/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30568/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + 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='> ' + INVOCATION_ID=fcc9a2ae22ef4bd1a23cd8402482182e + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=30568 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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.UmwjovkSYn/pbuilderrc_XHo9 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.UmwjovkSYn/b2 --logfile b2/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-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 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 + Linux i-capture-the-hostname 4.19.0-9-686-pae #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) i686 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 + -rwxr-xr-x 1 root root 1302248 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 38692 Mar 1 2019 cat + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 63268 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chown + -rwxr-xr-x 1 root root 153732 Mar 1 2019 cp + -rwxr-xr-x 1 root root 132820 Jan 18 2019 dash + -rwxr-xr-x 1 root root 120676 Mar 1 2019 date + -rwxr-xr-x 1 root root 92040 Mar 1 2019 dd + -rwxr-xr-x 1 root root 100620 Mar 1 2019 df + -rwxr-xr-x 1 root root 149736 Mar 1 2019 dir + -rwxr-xr-x 1 root root 79412 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 34532 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 34532 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 67700 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 30112 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 206392 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 100952 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 21916 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 79752 Mar 1 2019 ln + -rwxr-xr-x 1 root root 55400 Jul 27 2018 login + -rwxr-xr-x 1 root root 149736 Mar 1 2019 ls + -rwxr-xr-x 1 root root 112032 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 87972 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 79748 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 46916 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 42348 Jan 10 2019 more + -rwsr-xr-x 1 root root 50592 Jan 10 2019 mount + -rwxr-xr-x 1 root root 13724 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 157832 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38660 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 46852 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 75588 Mar 1 2019 rm + -rwxr-xr-x 1 root root 42756 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 22276 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jun 25 09:06 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 22 22:27 sh.distrib -> dash + -rwxr-xr-x 1 root root 34532 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 79652 Mar 1 2019 stty + -rwsr-xr-x 1 root root 71072 Jan 10 2019 su + -rwxr-xr-x 1 root root 34564 Mar 1 2019 sync + -rwxr-xr-x 1 root root 504024 Apr 24 2019 tar + -rwxr-xr-x 1 root root 13860 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 104292 Mar 1 2019 touch + -rwxr-xr-x 1 root root 34532 Mar 1 2019 true + -rwxr-xr-x 1 root root 17768 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 30108 Jan 10 2019 umount + -rwxr-xr-x 1 root root 34532 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 149736 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34208 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/30568/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -257,7 +293,7 @@ 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) +Fetched 26.0 MB in 7s (3472 kB/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.) @@ -468,7 +504,7 @@ 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 +I: Running cd /build/phast-1.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 @@ -535,7 +571,7 @@ 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 +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/chooseLines /build/phast-1.4+dfsg/src/util/../../bin/hmm_tweak /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/all_dists /build/phast-1.4+dfsg/src/util/../../bin/tree_doctor /build/phast-1.4+dfsg/src/util/../../bin/msa_diff /build/phast-1.4+dfsg/src/util/../../bin/indelFit /build/phast-1.4+dfsg/src/util/../../bin/consEntropy /build/phast-1.4+dfsg/src/util/../../bin/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/maf_parse /build/phast-1.4+dfsg/src/util/../../bin/msa_split /build/phast-1.4+dfsg/src/util/../../bin/modFreqs /build/phast-1.4+dfsg/src/util/../../bin/eval_predictions /build/phast-1.4+dfsg/src/util/../../bin/display_rate_matrix /build/phast-1.4+dfsg/src/util/../../bin/makeHKY /build/phast-1.4+dfsg/src/util/../../bin/phastBias /build/phast-1.4+dfsg/src/util/../../bin/refeature /build/phast-1.4+dfsg/src/util/../../bin/msa_view make[3]: Leaving directory '/build/phast-1.4+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/phast-1.4+dfsg/src' @@ -547,7 +583,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j18 + make -j10 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 ) @@ -568,11 +604,6 @@ : 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 @@ -593,7 +624,7 @@ : 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 +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 @@ -633,22 +664,27 @@ : 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 +gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c misc.c -o misc.o +: warning: "PHAST_HOME" redefined +: note: this is the location of the previous definition +: warning: "PHAST_HOME" redefined +: note: this is the location of the previous definition +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o ar: creating /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a -ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o 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 +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o +ar rs /build/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o make[4]: Leaving directory '/build/phast-1.4+dfsg/src/lib/base' make[4]: Entering directory '/build/phast-1.4+dfsg/src/lib/msa' gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c sufficient_stats.c -o sufficient_stats.o @@ -729,18 +765,18 @@ 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 +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 -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 +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 -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 +ar rs /build/phast-1.4+dfsg/src/lib/hmm/../../../lib/libphast.a hmm.o em.o +ar rs /build/phast-1.4+dfsg/src/lib/hmm/../../../lib/libphast.a hmm.o em.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 @@ -748,72 +784,72 @@ : 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 +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_history.c -o indel_history.o +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 phylo_fit.c -o phylo_fit.o +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_column.c -o fit_column.o +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 subst_mods.c -o subst_mods.o +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 fit_feature.c -o fit_feature.o +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 phast_cons.c -o phast_cons.o +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 indel_mod.c -o indel_mod.o +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 phylo_p.c -o phylo_p.o +gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_em.c -o fit_em.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_p_print.c -o phylo_p_print.o +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 trees.c -o trees.o +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 subst_distrib.c -o subst_distrib.o +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 fit_em.c -o fit_em.o +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 tree_model.c -o tree_model.o +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 @@ -843,22 +879,22 @@ 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 +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.o bgc_hmm.o +ar rs /build/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o indel_mod.o phylo_p.o phylo_p_print.o trees.o phylo_fit.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 @@ -1013,8 +1049,8 @@ 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 makeHKY.help_src > makeHKY.help ../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 @@ -1022,7 +1058,7 @@ ../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 indelFit.help_src > indelFit.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 @@ -1032,10 +1068,14 @@ : 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 +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/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now +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 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 draw_tree.c -o draw_tree.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition @@ -1052,10 +1092,10 @@ : 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 +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/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now +gcc -L/build/phast-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition @@ -1068,10 +1108,14 @@ : 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 +gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -L/build/phast-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now +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 stringiphy.c -o stringiphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition @@ -1088,14 +1132,6 @@ : 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 @@ -1104,14 +1140,14 @@ : 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 +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/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 +gcc -L/build/phast-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now +gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition -gcc -L/build/phast-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now +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 display_rate_matrix.c -o display_rate_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition @@ -1120,10 +1156,6 @@ 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 @@ -1136,6 +1168,10 @@ : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/build/phast-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now +gcc -g -O2 -ffile-prefix-map=/build/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/build/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/build/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/build/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o +: warning: "PHAST_HOME" redefined +: note: this is the location of the previous definition +gcc -L/build/phast-1.4+dfsg/src/util/../../lib -o /build/phast-1.4+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/phast-1.4+dfsg/src/util' mkdir -p ../doc/man/ Generating man pages... @@ -1196,7 +1232,7 @@ dh_testroot dh_prep dh_auto_install - make -j18 install DESTDIR=/build/phast-1.4\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no + make -j10 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' @@ -1221,26 +1257,28 @@ 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) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/phastMotif debian/phast/usr/bin/phast debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/dless debian/phast/usr/bin/phastCons debian/phast/usr/bin/msa_split debian/phast/usr/bin/stringiphy debian/phast/usr/bin/phastOdds debian/phast/usr/bin/refeature debian/phast/usr/bin/makeHKY debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/exoniphy debian/phast/usr/bin/indelHistory debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/clean_genes debian/phast/usr/bin/msa_view debian/phast/usr/bin/dlessP debian/phast/usr/bin/phyloP debian/phast/usr/bin/base_evolve debian/phast/usr/bin/phyloFit debian/phast/usr/bin/chooseLines debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/indelFit debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/draw_tree debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/maf_parse debian/phast/usr/bin/convert_coords debian/phast/usr/bin/treeGen debian/phast/usr/bin/hmm_train debian/phast/usr/bin/modFreqs debian/phast/usr/bin/msa_diff debian/phast/usr/bin/consEntropy debian/phast/usr/bin/phastBias debian/phast/usr/bin/all_dists debian/phast/usr/bin/hmm_view debian/phast/usr/bin/prequel were not linked against libtmglib.so.3 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/phastMotif debian/phast/usr/bin/phast debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/dless debian/phast/usr/bin/phastCons debian/phast/usr/bin/msa_split debian/phast/usr/bin/stringiphy debian/phast/usr/bin/phastOdds debian/phast/usr/bin/refeature debian/phast/usr/bin/makeHKY debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/exoniphy debian/phast/usr/bin/indelHistory debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/clean_genes debian/phast/usr/bin/msa_view debian/phast/usr/bin/dlessP debian/phast/usr/bin/phyloP debian/phast/usr/bin/base_evolve debian/phast/usr/bin/phyloFit debian/phast/usr/bin/chooseLines debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/indelFit debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/draw_tree debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/maf_parse debian/phast/usr/bin/convert_coords debian/phast/usr/bin/treeGen debian/phast/usr/bin/hmm_train debian/phast/usr/bin/modFreqs debian/phast/usr/bin/msa_diff debian/phast/usr/bin/consEntropy debian/phast/usr/bin/phastBias debian/phast/usr/bin/all_dists debian/phast/usr/bin/hmm_view debian/phast/usr/bin/prequel were not linked against libblas.so.3 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'phast' in '../phast_1.4+dfsg-1_i386.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.4+dfsg-1_i386.deb'. +dpkg-deb: building package 'phast' in '../phast_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: user script /srv/workspace/pbuilder/30568/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30568/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/39985 and its subdirectories -I: Current time: Tue Jul 27 13:27:06 -12 2021 -I: pbuilder-time-stamp: 1627435626 +I: removing directory /srv/workspace/pbuilder/30568 and its subdirectories +I: Current time: Thu Jun 25 09:13:41 +14 2020 +I: pbuilder-time-stamp: 1593026021