Diff of the two buildlogs: -- --- b1/build.log 2021-08-09 23:43:01.008644347 +0000 +++ b2/build.log 2021-08-09 23:57:09.888911169 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Sep 11 18:04:19 -12 2022 -I: pbuilder-time-stamp: 1662962659 +I: Current time: Tue Aug 10 13:43:12 +14 2021 +I: pbuilder-time-stamp: 1628552592 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./libvcflib_1.0.2+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.HgvmnuVD/trustedkeys.kbx': General error -gpgv: Signature made Thu Jan 28 00:04:01 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.mni_HwaF/trustedkeys.kbx': General error +gpgv: Signature made Fri Jan 29 02:04:01 2021 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libvcflib_1.0.2+dfsg-2.dsc @@ -38,137 +38,171 @@ dpkg-source: info: applying tests I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/17286/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/21242/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-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/21242/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/21242/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,-fixfilepath parallel=16' - 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]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=7' + 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='72d50c468ecb4d41acf6fb33efded3be' - 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='17286' - PS1='# ' - PS2='> ' + INVOCATION_ID=7093b4b0c3ad4dbcabbf587f84579bed + 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=21242 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.05ar4Uu361/pbuilderrc_1DVU --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.05ar4Uu361/b1 --logfile b1/build.log libvcflib_1.0.2+dfsg-2.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.05ar4Uu361/pbuilderrc_foVC --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.05ar4Uu361/b2 --logfile b2/build.log --extrapackages usrmerge libvcflib_1.0.2+dfsg-2.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 ionos6-i386 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-686-pae #1 SMP Debian 4.19.194-3 (2021-07-18) i686 GNU/Linux I: ls -l /bin - total 5776 - -rwxr-xr-x 1 root root 1367848 Aug 4 2021 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Jul 28 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Jul 28 2021 more - -rwsr-xr-x 1 root root 50720 Jul 28 2021 mount - -rwxr-xr-x 1 root root 13856 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 11 03:48 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Jul 28 2021 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Jul 28 2021 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/17286/tmp/hooks/D02_print_environment finished + total 5788 + -rwxr-xr-x 1 root root 1367848 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Jul 29 09:09 more + -rwsr-xr-x 1 root root 50720 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 13856 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 10 13:48 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 8 23:27 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Jul 29 09:09 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/21242/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -298,7 +332,7 @@ Get: 72 http://deb.debian.org/debian bullseye/main i386 libtabixpp-dev i386 1.1.0-4 [9108 B] Get: 73 http://deb.debian.org/debian bullseye/main i386 markdown all 1.0.1-10.1 [17.5 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 pkg-config i386 0.29.2-1 [66.3 kB] -Fetched 39.7 MB in 1s (37.1 MB/s) +Fetched 39.7 MB in 11s (3738 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19675 files and directories currently installed.) @@ -610,8 +644,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (438 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 25284 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/libvcflib-1.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/libvcflib-1.0.2+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 libvcflib dpkg-buildpackage: info: source version 1.0.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -702,7 +772,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/libvcflib-1.0.2+dfsg' dh_auto_build - cd obj-i686-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j7 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/libvcflib-1.0.2+dfsg -B/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -717,19 +787,19 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o -[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o +[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/Variant.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/Variant.cpp +[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/rnglib.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/rnglib.cpp /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/var.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/var.cpp -[ 3%] Building C object CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o +[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/cdflib.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/cdflib.cpp +[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/pdflib.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/pdflib.cpp +[ 4%] Building C object CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o /usr/bin/cc -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -c /build/libvcflib-1.0.2+dfsg/filevercmp/filevercmp.c -[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/Variant.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/Variant.cpp -[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o -[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/rnglib.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/rnglib.cpp [ 4%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/pdflib.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/pdflib.cpp /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/split.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/split.cpp [ 5%] Linking CXX shared library libvcflib.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vcflib.dir/link.txt --verbose=1 @@ -741,282 +811,324 @@ make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake --color= make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend +make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake --color= +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake --color= +make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfsample2info.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend -make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfevenregions.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend -make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg 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"/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcreatemulti.dir/depend.internal". +make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build +make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build +make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake" is newer than depender 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CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build -Scanning dependencies of target vcfgeno2haplo make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target vcf2fasta -Scanning dependencies of target vcfevenregions make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target vcfcreatemulti +[ 5%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfinfosummarize.cpp +[ 6%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o +[ 7%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcf2dag.cpp +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgenosummarize.cpp +[ 8%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 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-DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfsample2info.cpp +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfglbound.cpp +[ 11%] Linking CXX executable vcfindex +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1 +[ 12%] Linking CXX executable vcfglbound +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglbound.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -o vcfindex -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 12%] Built target vcfindex +make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend +[ 12%] Built target vcfglbound +make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcheck.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcheck.dir/depend.internal". -make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfevenregions.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfevenregions.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfevenregions.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfevenregions.dir/depend.internal". +Scanning dependencies of target vcfevenregions make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcreatemulti.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcreatemulti.dir/depend.internal". +Scanning dependencies of target vcfcreatemulti make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build -make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfevenregions.cpp +[ 13%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcreatemulti.cpp +[ 13%] Linking CXX executable vcfsample2info +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 14%] Linking CXX executable vcfinfosummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfosummarize.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 14%] Built target vcfsample2info +make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcombine.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcombine.dir/depend.internal". +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfbreakmulti.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfbreakmulti.dir/depend.internal". +Scanning dependencies of target vcfbreakmulti +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 6%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -[ 7%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcf2dag.cpp -[ 7%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -[ 8%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfindex.cpp -[ 8%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfglbound.cpp -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgenosummarize.cpp -[ 9%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -[ 9%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgeno2haplo.cpp -[ 10%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfinfosummarize.cpp +[ 14%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfbreakmulti.cpp -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfsample2info.cpp -[ 10%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfremap.cpp -[ 11%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfevenregions.cpp -[ 12%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -[ 12%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 14%] Built target vcfinfosummarize +make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2fasta.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2fasta.dir/depend.internal". +Scanning dependencies of target vcf2fasta +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 15%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcf2fasta.cpp -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcreatemulti.cpp -Scanning dependencies of target vcfcheck -Scanning dependencies of target vcfuniq -Scanning dependencies of target vcfcombine +[ 15%] Linking CXX executable vcf2dag +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 +[ 16%] Linking CXX executable vcfgenosummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -o vcfgenosummarize -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 16%] Built target vcf2dag +[ 16%] Built target vcfgenosummarize +make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend +make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu 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of target vcfremap Scanning dependencies of target vcfuniqalleles make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 17%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o +[ 17%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfuniqalleles.cpp +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfremap.cpp +[ 17%] Linking CXX executable vcfevenregions +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 17%] Built target vcfevenregions +make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfuniq.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfuniq.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfuniq.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfuniq.dir/depend.internal". +Scanning dependencies of target vcfuniq make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build +[ 18%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfuniq.cpp +[ 18%] Linking CXX executable vcfuniqalleles +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -o vcfuniqalleles -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 18%] Built target vcfuniqalleles +make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcheck.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcheck.dir/depend.internal". +Scanning dependencies of target vcfcheck +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build -make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 18%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcheck.cpp +[ 19%] Linking CXX executable vcfbreakmulti +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 19%] Built target vcfbreakmulti +make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcombine.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcombine.dir/depend.internal". +Scanning dependencies of target vcfcombine +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 13%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfuniq.cpp -[ 14%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -[ 14%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfuniqalleles.cpp -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcheck.cpp -[ 15%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o +[ 20%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcombine.cpp -[ 15%] Linking CXX executable vcfuniq -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 16%] Linking CXX executable vcfcheck -/usr/bin/cmake -E cmake_link_script 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-rdynamic CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 21%] Linking CXX executable vcf2fasta +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 16%] Built target vcfcheck -[ 16%] Built target vcfuniq +[ 21%] Built target vcfcreatemulti make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfroc.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfroc.dir/depend.internal". +Scanning dependencies of target vcfroc +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 22%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfroc.cpp +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 22%] Built target vcf2fasta make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfroc.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfroc.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenotypes.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenotypes.dir/depend.internal". -[ 17%] Linking CXX executable vcfindex -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1 -[ 17%] Linking CXX executable vcfuniqalleles -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -o vcfindex -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -o vcfuniqalleles -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 17%] Linking CXX executable vcfevenregions -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -Scanning dependencies of target vcfroc Scanning dependencies of target vcfgenotypes make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 18%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -[ 18%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfroc.cpp +[ 22%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgenotypes.cpp +[ 22%] Linking CXX executable vcfuniq +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 22%] Linking CXX executable vcfgeno2haplo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 +[ 23%] Linking CXX executable vcfremap +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -o vcfgeno2haplo -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -o vcfremap -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 18%] Built target vcfindex +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 23%] Built target vcfgeno2haplo make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 23%] Built target vcfuniq make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake --color= -[ 18%] Built target vcfuniqalleles -Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfqual2info.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfqual2info.dir/depend.internal". make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend -Scanning dependencies of target vcfqual2info make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake --color= +[ 23%] Built target vcfremap +make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfqual2info.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfqual2info.dir/depend.internal". +Scanning dependencies of target vcfqual2info make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfstreamsort.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfstreamsort.dir/depend.internal". -[ 19%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/abba-baba.dir/DependInfo.cmake --color= Scanning dependencies of target vcfstreamsort -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfqual2info.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 20%] Linking CXX executable vcfglbound -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglbound.dir/link.txt --verbose=1 -[ 20%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -[ 20%] Built target vcfevenregions -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfstreamsort.cpp -make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend +make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/abba-baba.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 24%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/abba-baba.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/abba-baba.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/abba-baba.dir/depend.internal". +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfqual2info.cpp Scanning dependencies of target abba-baba make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/build +[ 24%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfstreamsort.cpp make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 20%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o +[ 24%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/abba-baba.cpp +[ 25%] Linking CXX executable vcfcheck +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 20%] Built target vcfglbound +[ 25%] Built target vcfcheck make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/depend -[ 20%] Linking CXX executable vcfsample2info -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/segmentFst.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/segmentFst.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/segmentFst.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/segmentFst.dir/depend.internal". Scanning dependencies of target segmentFst make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 20%] Building CXX object CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o +[ 25%] Building CXX object CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/segmentFst.cpp -[ 21%] Linking CXX executable vcfinfosummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfosummarize.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 26%] Linking CXX executable vcfgenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 21%] Built target vcfsample2info +[ 26%] Built target vcfgenotypes make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake --color= @@ -1026,26 +1138,29 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 22%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o +[ 27%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfhethomratio.cpp +[ 28%] Linking CXX executable segmentFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -o segmentFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 22%] Built target vcfinfosummarize +[ 28%] Built target segmentFst make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake --color= -[ 22%] Linking CXX executable vcf2dag -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/meltEHH.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/meltEHH.dir/depend.internal". Scanning dependencies of target meltEHH make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 23%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o +[ 29%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/meltEHH.cpp +[ 29%] Linking CXX executable vcfqual2info +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfqual2info.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 23%] Built target vcf2dag +[ 29%] Built target vcfqual2info make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcffilter.dir/DependInfo.cmake --color= @@ -1055,29 +1170,32 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 24%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o +[ 30%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcffilter.cpp -[ 25%] Linking CXX executable vcfgenosummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -o vcfgenosummarize -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 31%] Linking CXX executable abba-baba +/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -o abba-baba -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 26%] Linking CXX executable vcfbreakmulti -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 -[ 26%] Built target vcfgenosummarize +[ 31%] Built target abba-baba make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfclassify.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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Scanning dependencies of target vcfclassify make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 27%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o +[ 32%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfclassify.cpp +[ 32%] Linking CXX executable vcfcombine +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 32%] Linking CXX executable vcfhethomratio +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 27%] Built target vcfbreakmulti +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 32%] Built target vcfcombine make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake --color= @@ -1087,13 +1205,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 27%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o +[ 32%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfaddinfo.cpp -[ 28%] Linking CXX executable vcfremap -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -o vcfremap -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 28%] Built target vcfremap +[ 32%] Built target vcfhethomratio make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake --color= @@ -1102,14 +1217,14 @@ Scanning dependencies of target vcfgenosamplenames make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build +[ 33%] Linking CXX executable vcfstreamsort make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstreamsort.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 34%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgenosamplenames.cpp -[ 30%] Linking CXX executable segmentFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -o segmentFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 30%] Built target segmentFst +[ 34%] Built target vcfstreamsort make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfaltcount.dir/DependInfo.cmake --color= @@ -1119,16 +1234,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 31%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o +[ 35%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfaltcount.cpp -[ 32%] Linking CXX executable vcfcreatemulti -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 32%] Linking CXX executable vcf2fasta -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 35%] Linking CXX executable vcfclassify +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -o vcfclassify -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 32%] Built target vcfcreatemulti +[ 35%] Built target vcfclassify make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfhetcount.dir/DependInfo.cmake --color= @@ -1138,10 +1250,16 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 33%] Building CXX object CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o +[ 36%] Building CXX object CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfhetcount.cpp +[ 37%] Linking CXX executable vcffilter +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 37%] Linking CXX executable vcfgenosamplenames +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 33%] Built target vcf2fasta +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 37%] Built target vcffilter make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/pFst.dir/DependInfo.cmake --color= @@ -1151,77 +1269,74 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 33%] Linking CXX executable vcfqual2info -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfqual2info.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 33%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o +[ 37%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/pFst.dir/src/pFst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/pFst.cpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 33%] Built target vcfqual2info +[ 37%] Linking CXX executable vcfaltcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 +[ 37%] Built target vcfgenosamplenames make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/plotHaps.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp 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Scanning dependencies of target plotHaps make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 34%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o +[ 38%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/plotHaps.cpp -[ 35%] Linking CXX executable vcfgenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 35%] Built target vcfgenotypes +[ 39%] Linking CXX executable vcfaddinfo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1 +[ 39%] Built target vcfaltcount make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend +[ 40%] Linking CXX executable meltEHH +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -o vcfaddinfo -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +/usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -o meltEHH -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 40%] Linking CXX executable vcfroc +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfinfo2qual.dir/depend.internal". 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Scanning dependencies of target vcfinfo2qual make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 35%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 40%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfinfo2qual.cpp -[ 35%] Linking CXX executable vcfcombine -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 35%] Linking CXX executable vcfhethomratio -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 35%] Built target vcfcombine +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 40%] Built target vcfaddinfo +[ 40%] Built target meltEHH make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/depend +make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfld.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/smoother.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfld.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfld.dir/depend.internal". 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Scanning dependencies of target smoother make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 37%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/smoother.dir/src/smoother.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/smoother.cpp -[ 37%] Linking CXX executable vcfclassify -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -o vcfclassify -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 37%] Built target vcfclassify +[ 41%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfld.dir/src/vcfld.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfld.cpp +[ 42%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/smoother.dir/src/smoother.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/smoother.cpp +[ 42%] Built target vcfroc make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake --color= @@ -1231,61 +1346,61 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 37%] Building CXX object CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o +[ 42%] Building CXX object CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfremovesamples.cpp -[ 38%] Linking CXX executable vcfaddinfo -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1 -[ 38%] Linking CXX executable vcfgenosamplenames -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -o vcfaddinfo -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 42%] Linking CXX executable vcfhetcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 38%] Built target vcfaddinfo +[ 42%] Built target vcfhetcount make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfprimers.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfprimers.dir/depend.internal". Scanning dependencies of target vcfprimers -[ 38%] Built target vcfgenosamplenames make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfprimers.cpp +[ 44%] Linking CXX executable vcfinfo2qual +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfo2qual.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -o vcfinfo2qual -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 44%] Built target vcfinfo2qual make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake --color= -[ 39%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfprimers.cpp Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfrandom.dir/depend.internal". 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Scanning dependencies of target vcfrandom make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 40%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o +[ 45%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfrandom.cpp -[ 40%] Linking CXX executable vcfaltcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 45%] Linking CXX executable smoother +/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 40%] Built target vcfaltcount +[ 45%] Built target smoother make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/iHS.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/iHS.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/iHS.dir/depend.internal". 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-Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 47%] Building CXX object CMakeFiles/iHS.dir/src/iHS.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/iHS.dir/src/iHS.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/iHS.cpp -[ 42%] Linking CXX executable abba-baba -/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -o abba-baba -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 42%] Built target abba-baba +[ 47%] Built target vcfremovesamples make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 45%] Linking CXX executable vcfhetcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 +[ 49%] Linking CXX executable pFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 45%] Linking CXX executable vcfgeno2haplo -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 -[ 45%] Built target vcfinfo2qual +[ 49%] Linking CXX executable plotHaps +/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 +[ 49%] Built target pFst make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -o plotHaps -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu 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Scanning dependencies of target vcfafpath make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 45%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o +[ 49%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfafpath.cpp +[ 49%] Linking CXX executable vcfprimers +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 45%] Built target vcfstreamsort +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 49%] Built target plotHaps make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfecho.dir/DependInfo.cmake --color= @@ -1333,13 +1445,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o +[ 50%] Building CXX object CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfecho.cpp -[ 46%] Linking CXX executable smoother make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 46%] Built target vcfhetcount +[ 50%] Built target vcfprimers make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/genotypeSummary.dir/DependInfo.cmake --color= @@ -1349,10 +1458,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 47%] Building CXX object CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o +[ 51%] Building CXX object CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/genotypeSummary.cpp +[ 52%] Linking CXX executable vcfld +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 47%] Built target vcfgeno2haplo +[ 52%] Built target vcfld make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake --color= @@ -1362,26 +1474,29 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 47%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o +[ 52%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfsitesummarize.cpp +[ 52%] Linking CXX executable vcfrandom +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 47%] Built target smoother +[ 52%] Built target vcfrandom make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcommonsamples.dir/depend.internal". 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Scanning dependencies of target vcfcommonsamples +[ 52%] Linking CXX executable vcfkeepgeno make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1 make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 48%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 53%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcommonsamples.cpp -[ 49%] Linking CXX executable meltEHH -/usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -o meltEHH -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 49%] Built target meltEHH +[ 53%] Built target vcfkeepgeno make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/bFst.dir/DependInfo.cmake --color= @@ -1391,19 +1506,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 49%] Building CXX object CMakeFiles/bFst.dir/src/bFst.cpp.o +[ 53%] Building CXX object CMakeFiles/bFst.dir/src/bFst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/bFst.dir/src/bFst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/bFst.cpp -[ 50%] Linking CXX executable vcfremovesamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -o vcfremovesamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 51%] Linking CXX executable vcffilter -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 53%] Linking CXX executable vcfecho +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 51%] Linking CXX executable vcfprimers -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 -[ 51%] Built target vcfremovesamples -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 53%] Built target vcfecho make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfentropy.dir/DependInfo.cmake --color= @@ -1413,25 +1522,31 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 52%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o +[ 54%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfentropy.cpp +[ 54%] Linking CXX executable iHS +/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 55%] Linking CXX executable vcfafpath +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 52%] Built target vcffilter +[ 55%] Built target vcfafpath make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu 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Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/permuteSmooth.dir/depend.internal". Scanning dependencies of target permuteSmooth make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 52%] Built target vcfprimers -make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake --color= -[ 53%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 56%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/permuteSmooth.cpp Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/depend.internal". @@ -1439,77 +1554,77 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 53%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o +[ 56%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfremoveaberrantgenotypes.cpp -[ 53%] Linking CXX executable vcfkeepgeno -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 57%] Linking CXX executable vcfsitesummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 58%] Linking CXX executable vcfcommonsamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 53%] Built target vcfkeepgeno +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 58%] Built target vcfcommonsamples make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/pVst.dir/DependInfo.cmake --color= +[ 58%] Built target vcfsitesummarize +make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/pVst.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/pVst.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/pVst.dir/depend.internal". Scanning dependencies of target pVst -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 53%] Building CXX object CMakeFiles/pVst.dir/src/pVst.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/pVst.dir/src/pVst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/pVst.cpp -[ 53%] Linking CXX executable vcfecho -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 54%] Linking CXX executable pFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 54%] Linking CXX executable vcfrandom -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 54%] Built target vcfecho -make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend +make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/permuteGPAT++.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/permuteGPAT++.dir/depend.internal". Scanning dependencies of target permuteGPAT++ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/build +[ 58%] Building CXX object CMakeFiles/pVst.dir/src/pVst.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/pVst.dir/src/pVst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/pVst.cpp make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 55%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o +[ 59%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/permuteGPAT++.cpp -[ 55%] Built target pFst +[ 59%] Linking CXX executable genotypeSummary +/usr/bin/cmake -E cmake_link_script CMakeFiles/genotypeSummary.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -o genotypeSummary -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 59%] Linking CXX executable permuteSmooth +/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 59%] Built target genotypeSummary make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend +[ 59%] Built target permuteSmooth +make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/depend.internal". -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' Scanning dependencies of target dumpContigsFromHeader make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 55%] Built target vcfrandom -make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color= -[ 55%] Building CXX object CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/dumpContigsFromHeader.cpp Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/depend.internal". Scanning dependencies of target vcfgenotypecompare +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 55%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o +[ 59%] Building CXX object CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o +[ 59%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/dumpContigsFromHeader.cpp /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgenotypecompare.cpp -[ 55%] Linking CXX executable plotHaps -/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -o plotHaps -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 59%] Linking CXX executable permuteGPAT++ +/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 55%] Built target plotHaps +[ 59%] Built target permuteGPAT++ make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake --color= @@ -1519,19 +1634,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 55%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o +[ 59%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfflatten.cpp -[ 56%] Linking CXX executable vcfcommonsamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 57%] Linking CXX executable vcfsitesummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 57%] Linking CXX executable permuteSmooth -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 59%] Linking CXX executable vcfentropy +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 57%] Built target vcfcommonsamples +[ 59%] Built target vcfentropy make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfannotate.dir/DependInfo.cmake --color= @@ -1541,24 +1650,30 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 58%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o +[ 60%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfannotate.cpp +[ 61%] Linking CXX executable vcfremoveaberrantgenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 62%] Linking CXX executable dumpContigsFromHeader +/usr/bin/cmake -E cmake_link_script CMakeFiles/dumpContigsFromHeader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -o dumpContigsFromHeader -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 58%] Built target vcfsitesummarize +[ 62%] Built target vcfremoveaberrantgenotypes make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/hapLrt.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/hapLrt.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/hapLrt.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/hapLrt.dir/depend.internal". Scanning dependencies of target hapLrt make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 58%] Built target permuteSmooth -make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend -[ 59%] Building CXX object CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o +[ 63%] Building CXX object CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/hapLrt.cpp +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 63%] Built target dumpContigsFromHeader +make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfkeepsamples.dir/depend.internal". @@ -1567,33 +1682,33 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 60%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o +[ 64%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfkeepsamples.cpp -[ 61%] Linking CXX executable vcfafpath -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 61%] Linking CXX executable permuteGPAT++ -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 65%] Linking CXX executable bFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 61%] Built target vcfafpath +[ 65%] Built target bFst make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/normalize-iHS.dir/DependInfo.cmake --color= -[ 62%] Linking CXX executable vcfld Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/normalize-iHS.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/normalize-iHS.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/normalize-iHS.dir/depend.internal". -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 Scanning dependencies of target normalize-iHS make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 62%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o +[ 65%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/normalize-iHS.cpp +[ 66%] Linking CXX executable normalize-iHS +/usr/bin/cmake -E cmake_link_script CMakeFiles/normalize-iHS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -o normalize-iHS -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 62%] Built target permuteGPAT++ +[ 66%] Linking CXX executable vcfkeepsamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 +[ 66%] Built target normalize-iHS make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2tsv.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2tsv.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2tsv.dir/depend.internal". @@ -1602,74 +1717,77 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 63%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o +[ 67%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcf2tsv.cpp +[ 68%] Linking CXX executable pVst +/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 63%] Built target vcfld +[ 69%] Linking CXX executable vcfflatten +[ 69%] Built target vcfkeepsamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfflatten.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/popStats.dir/DependInfo.cmake --color= -[ 63%] Linking CXX executable vcfroc -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/popStats.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/popStats.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/popStats.dir/depend.internal". Scanning dependencies of target popStats make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 64%] Building CXX object CMakeFiles/popStats.dir/src/popStats.cpp.o +[ 70%] Building CXX object CMakeFiles/popStats.dir/src/popStats.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/popStats.dir/src/popStats.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/popStats.cpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 64%] Built target vcfroc +[ 70%] Built target pVst make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcat.dir/DependInfo.cmake --color= +[ 70%] Built target vcfflatten +make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/sequenceDiversity.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcat.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcat.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcat.dir/depend.internal". Scanning dependencies of target vcfcat make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 64%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o +[ 70%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcat.cpp -[ 64%] Linking CXX executable vcfentropy -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 65%] Linking CXX executable vcfremoveaberrantgenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 66%] Linking CXX executable dumpContigsFromHeader -/usr/bin/cmake -E cmake_link_script CMakeFiles/dumpContigsFromHeader.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -o dumpContigsFromHeader -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 66%] Built target vcfentropy -make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/sequenceDiversity.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/sequenceDiversity.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/sequenceDiversity.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/sequenceDiversity.dir/depend.internal". 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+1797,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 67%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcffixup.cpp -[ 67%] Linking CXX executable iHS -/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 67%] Built target iHS +[ 73%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcffixup.cpp +[ 73%] Built target vcfcat make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake --color= @@ -1695,45 +1810,45 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfsamplediff.dir/build.make 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CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -o normalize-iHS -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 75%] Linking CXX executable vcf2tsv +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 75%] Linking CXX executable vcfannotate +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -o vcfannotate -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 76%] Linking CXX executable vcfsamplenames +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 70%] Linking CXX executable bFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 -[ 70%] Built target genotypeSummary -[ 70%] Built target normalize-iHS +[ 76%] Built target vcf2tsv make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color= +[ 76%] Built target vcfannotate make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfstats.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfparsealts.dir/depend.internal". 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'/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 70%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o +[ 76%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfparsealts.cpp -[ 70%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o +[ 76%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfstats.cpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 70%] Built target bFst +[ 76%] Built target vcfsamplenames make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfnumalt.dir/DependInfo.cmake --color= @@ -1743,13 +1858,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 70%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o +[ 76%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfnumalt.cpp -[ 70%] Linking CXX executable vcfkeepsamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 77%] Linking CXX executable popStats +/usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/wcFst.dir/DependInfo.cmake --color= @@ -1759,13 +1874,19 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 71%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o +[ 78%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 79%] Linking CXX executable sequenceDiversity +/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 80%] Linking CXX executable vcfparsealts +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -o vcfparsealts -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 72%] Built target vcfsamplenames +[ 80%] Built target vcfsamplediff make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake --color= @@ -1775,13 +1896,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 73%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o +[ 81%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcleancomplex.cpp -[ 74%] Linking CXX executable vcfcat -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 74%] Built target vcfcat +[ 81%] Built target sequenceDiversity make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake --color= @@ -1791,13 +1909,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 74%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o +[ 81%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfleftalign.cpp -[ 75%] Linking CXX executable vcf2tsv -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 82%] Linking CXX executable vcffixup +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 75%] Built target vcf2tsv +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -o vcffixup -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 82%] Built target vcfparsealts make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake --color= @@ -1807,19 +1925,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o +[ 83%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfglxgt.cpp -[ 77%] Linking CXX executable vcfflatten -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfflatten.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 78%] Linking CXX executable pVst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 79%] Linking CXX executable vcfparsealts -/usr/bin/cmake -E cmake_link_script 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/build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfintersect.dir/DependInfo.cmake --color= @@ -1829,71 +1938,77 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 79%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o +[ 83%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfintersect.cpp +[ 84%] Linking CXX executable vcfnumalt +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 79%] Built target pVst +[ 84%] Built target vcfnumalt make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend -[ 79%] Built target vcfparsealts -make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg 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Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/depend.internal". Scanning dependencies of target vcfallelicprimitives -Scanning dependencies of target vcfannotategenotypes make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 85%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfallelicprimitives.cpp +[ 85%] Linking CXX executable vcfcleancomplex +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -o vcfcleancomplex -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build +[ 85%] Built target vcfcleancomplex +make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/depend.internal". +Scanning dependencies of target vcfannotategenotypes +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 80%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfallelicprimitives.cpp -[ 81%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o +[ 86%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfannotategenotypes.cpp -[ 82%] Linking CXX executable vcffixup -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 -[ 83%] Linking CXX executable vcfnumalt -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -o vcffixup -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 83%] Linking CXX executable vcfsamplediff -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.dir/link.txt --verbose=1 +[ 86%] Linking CXX executable vcfglxgt +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglxgt.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfoverlay.cpp -[ 84%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o +[ 88%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfkeepinfo.cpp +[ 89%] Linking CXX executable vcfstats +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -o vcfstats -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 84%] Built target vcfsamplediff +[ 89%] Built target vcfstats make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake --color= @@ -1903,19 +2018,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 85%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o +[ 90%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgeno2alleles.cpp -[ 86%] Linking CXX executable popStats -/usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1 -[ 86%] Linking CXX executable hapLrt -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/popStats.dir/src/popStats.cpp.o -o popStats -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 86%] Linking CXX executable vcfcleancomplex -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -o vcfcleancomplex -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 91%] Linking CXX executable vcfleftalign +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 86%] Built target popStats +[ 91%] Built target vcfleftalign make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake --color= @@ -1925,40 +2034,49 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 86%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o +[ 91%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcountalleles.cpp -[ 86%] Built target hapLrt +[ 91%] Linking CXX executable vcfkeepinfo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. 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Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfdistance.dir/depend.internal". Scanning dependencies of target vcfdistance make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 86%] Built target vcfcleancomplex +[ 91%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfdistance.cpp +[ 91%] Linking CXX executable vcfgeno2alleles +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[ 91%] Built target vcfgeno2alleles make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake --color= -[ 86%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfdistance.cpp Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcflength.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcflength.dir/depend.internal". Scanning dependencies of target vcflength make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 86%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o +[ 91%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcflength.dir/src/vcflength.cpp.o -c 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-D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 86%] Built target vcfannotate +[ 93%] Linking CXX executable vcfoverlay +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 +[ 93%] Built target vcfcountalleles make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/depend +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -o vcfoverlay -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/segmentIhs.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/segmentIhs.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/segmentIhs.dir/depend.internal". @@ -1967,16 +2085,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 87%] Linking CXX executable sequenceDiversity -[ 87%] Building CXX object CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 +[ 93%] Building CXX object CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/segmentIhs.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 88%] Linking CXX executable vcfgenotypecompare -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 88%] Built target sequenceDiversity +[ 93%] Built target vcfoverlay make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake --color= @@ -1986,84 +2098,42 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o +[ 94%] Building CXX object CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfrandomsample.cpp +[ 95%] Linking CXX executable vcfdistance +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -o vcfdistance -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 89%] Built target vcfgenotypecompare -[ 90%] Linking CXX executable wcFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 90%] Built target wcFst -[ 90%] Linking CXX executable vcfglxgt -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglxgt.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 90%] Linking CXX executable vcfgeno2alleles -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 90%] Linking CXX executable vcfkeepinfo -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -o vcfkeepinfo -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 90%] Built target vcfglxgt -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 90%] Built target vcfgeno2alleles -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 90%] Built target vcfkeepinfo -[ 91%] Linking CXX executable vcfcountalleles -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 91%] Built target vcfcountalleles -[ 92%] Linking CXX executable segmentIhs +[ 95%] Built target vcfdistance +[ 96%] Linking CXX executable segmentIhs /usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -o segmentIhs -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 92%] Built target segmentIhs -[ 93%] Linking CXX executable vcfdistance -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -o vcfdistance -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 93%] Built target vcfdistance -[ 94%] Linking CXX executable vcflength +[ 96%] Built target segmentIhs +[ 97%] Linking CXX executable vcflength /usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcflength.dir/src/vcflength.cpp.o -o vcflength -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 98%] Linking CXX executable vcfintersect +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 94%] Built target vcflength -[ 95%] Linking CXX executable vcfstats -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -o vcfstats -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 95%] Built target vcfstats -[ 96%] Linking CXX executable vcfoverlay -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -o vcfoverlay -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 96%] Built target vcfoverlay -[ 97%] Linking CXX executable vcfleftalign -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 97%] Built target vcfleftalign -[ 98%] Linking CXX executable vcfrandomsample -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 98%] Built target vcflength make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[ 98%] Built target vcfrandomsample +[ 98%] Built target vcfintersect [ 99%] Linking CXX executable vcfannotategenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -o vcfannotategenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' [ 99%] Built target vcfannotategenotypes -[100%] Linking CXX executable vcfintersect -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' -[100%] Built target vcfintersect +[100%] Linking CXX executable vcfrandomsample +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [100%] Linking CXX executable vcfallelicprimitives /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -o vcfallelicprimitives -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' +[100%] Built target vcfrandomsample +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' [100%] Built target vcfallelicprimitives make[3]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu/CMakeFiles 0 @@ -2080,22 +2150,22 @@ [----------] Global test environment set-up. [----------] 1 test from Variant [ RUN ] Variant.correctGenotype -[ OK ] Variant.correctGenotype (3106 ms) -[----------] 1 test from Variant (3106 ms total) +[ OK ] Variant.correctGenotype (6629 ms) +[----------] 1 test from Variant (6629 ms total) [----------] 4 tests from VariantCallFile [ RUN ] VariantCallFile.open -[ OK ] VariantCallFile.open (0 ms) +[ OK ] VariantCallFile.open (2 ms) [ RUN ] VariantCallFile.recordCountUncompressed -[ OK ] VariantCallFile.recordCountUncompressed (0 ms) +[ OK ] VariantCallFile.recordCountUncompressed (1 ms) [ RUN ] VariantCallFile.recordCountCompressed -[ OK ] VariantCallFile.recordCountCompressed (4 ms) +[ OK ] VariantCallFile.recordCountCompressed (9 ms) [ RUN ] VariantCallFile.sampleNamesCompressed -[ OK ] VariantCallFile.sampleNamesCompressed (2 ms) -[----------] 4 tests from VariantCallFile (6 ms total) +[ OK ] VariantCallFile.sampleNamesCompressed (4 ms) +[----------] 4 tests from VariantCallFile (16 ms total) [----------] Global test environment tear-down -[==========] 5 tests from 2 test suites ran. (3112 ms total) +[==========] 5 tests from 2 test suites ran. (6645 ms total) [ PASSED ] 5 tests. make[2]: Leaving directory '/build/libvcflib-1.0.2+dfsg/test' make[1]: Leaving directory '/build/libvcflib-1.0.2+dfsg' @@ -2103,7 +2173,7 @@ dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake - cd obj-i686-linux-gnu && make -j16 install DESTDIR=/build/libvcflib-1.0.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j7 install DESTDIR=/build/libvcflib-1.0.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/libvcflib-1.0.2+dfsg -B/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2301,90 +2371,90 @@ -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/include/vec128int.h -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/include/veclib_types.h -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcountalleles.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfstreamsort.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfinfo2qual.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/bFst.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/wcFst.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/meltEHH.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcombine.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2fasta.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfrandom.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/permuteSmooth.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfkeepinfo.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfannotate.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsamplediff.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfannotategenotypes.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfstats.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsample2info.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfallelicprimitives.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/abba-baba.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfbreakmulti.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfprimers.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgeno2haplo.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/permuteGPAT++.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenosummarize.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfinfosummarize.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcreatemulti.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfleftalign.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcombine.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/plotHaps.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/sequenceDiversity.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/dumpContigsFromHeader.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfnumalt.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfuniqalleles.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfremovesamples.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfkeepgeno.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfhethomratio.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfecho.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/normalize-iHS.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/pFst.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/popStats.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfroc.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenotypes.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfflatten.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfkeepsamples.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2tsv.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/iHS.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfld.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfdistance.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcflength.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfkeepsamples.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgeno2haplo.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfglbound.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcat.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/meltEHH.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcountalleles.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/genotypeSummary.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsamplediff.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcffilter.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcheck.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfentropy.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfhethomratio.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2dag.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/permuteGPAT++.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfevenregions.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcommonsamples.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgeno2alleles.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfhetcount.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfqual2info.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcflib.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfbreakmulti.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfrandomsample.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcffixup.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/popStats.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/smoother.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/dumpContigsFromHeader.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfnumalt.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfintersect.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenotypecompare.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsitesummarize.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/iHS.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfparsealts.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfclassify.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2dag.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcflib.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/segmentIhs.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsamplenames.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfinfosummarize.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgeno2alleles.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfoverlay.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenotypecompare.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfevenregions.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfuniq.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfaddinfo.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfglxgt.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfglbound.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcffilter.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfintersect.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfleftalign.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/hapLrt.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/pVst.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/segmentFst.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcflength.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/plotHaps.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcat.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcheck.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsamplenames.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfrandom.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfaltcount.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenosamplenames.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfafpath.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/pVst.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfkeepinfo.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfremoveaberrantgenotypes.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/segmentIhs.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcffixup.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfqual2info.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenosamplenames.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfindex.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfentropy.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsample2info.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfflatten.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfparsealts.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfclassify.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/segmentFst.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfecho.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/permuteSmooth.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfannotate.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/bFst.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfafpath.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfuniqalleles.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfinfo2qual.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfstreamsort.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfrandomsample.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfallelicprimitives.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfglxgt.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/pFst.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfdistance.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/abba-baba.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfstats.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/wcFst.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenotypes.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfhetcount.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2fasta.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfkeepgeno.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/normalize-iHS.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/hapLrt.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcleancomplex.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfremovesamples.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenosummarize.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfremap.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/smoother.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2tsv.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfroc.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfannotategenotypes.1 make[1]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-i686-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/libvcflib-1.0.2+dfsg' @@ -2427,22 +2497,24 @@ dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.2+dfsg-2_i386.deb'. -dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.2+dfsg-2_i386.deb'. dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.2+dfsg-2_i386.deb'. -dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.2+dfsg-2_i386.deb'. dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.2+dfsg-2_i386.deb'. +dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.2+dfsg-2_i386.deb'. +dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.2+dfsg-2_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libvcflib_1.0.2+dfsg-2_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/21242/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/21242/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/17286 and its subdirectories -I: Current time: Sun Sep 11 18:06:00 -12 2022 -I: pbuilder-time-stamp: 1662962760 +I: removing directory /srv/workspace/pbuilder/21242 and its subdirectories +I: Current time: Tue Aug 10 13:57:09 +14 2021 +I: pbuilder-time-stamp: 1628553429