Diff of the two buildlogs: -- --- b1/build.log 2021-12-29 16:48:04.827530156 +0000 +++ b2/build.log 2021-12-29 16:50:10.931585606 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 31 11:08:41 -12 2023 -I: pbuilder-time-stamp: 1675206521 +I: Current time: Thu Dec 30 06:48:06 +14 2021 +I: pbuilder-time-stamp: 1640796486 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ 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.Kqyn2lcs/trustedkeys.kbx': General error -gpgv: Signature made Thu Jan 28 00:04:01 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.Ocee0CGo/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 @@ -37,135 +37,169 @@ dpkg-source: info: applying tests I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3605696/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/480769/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/480769/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/480769/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='e5af9c3758f64a0ab980a57896d48b44' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3605696' - PS1='# ' - PS2='> ' + INVOCATION_ID=b89a46f60b7349a4b94f09cafc2eea70 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=480769 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.xd6uW2oBOf/pbuilderrc_QB7N --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.xd6uW2oBOf/b1 --logfile b1/build.log libvcflib_1.0.2+dfsg-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - 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.xd6uW2oBOf/pbuilderrc_0kpi --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.xd6uW2oBOf/b2 --logfile b2/build.log libvcflib_1.0.2+dfsg-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 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 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 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 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 2021 more - -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount - -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 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 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 23 03:47 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 2021 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 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/3605696/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 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 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more + -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Dec 30 06:48 sh -> bash + lrwxrwxrwx 1 root root 4 Dec 21 23:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/480769/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -295,7 +329,7 @@ Get: 72 http://deb.debian.org/debian bullseye/main amd64 libtabixpp-dev amd64 1.1.0-4 [8288 B] Get: 73 http://deb.debian.org/debian bullseye/main amd64 markdown all 1.0.1-10.1 [17.5 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] -Fetched 36.5 MB in 1s (70.4 MB/s) +Fetched 36.5 MB in 1s (60.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19655 files and directories currently installed.) @@ -608,7 +642,8 @@ Building tag database... -> Finished parsing the build-deps 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libvcflib_1.0.2+dfsg-2_source.changes +hostname: Name or service not known +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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libvcflib_1.0.2+dfsg-2_source.changes dpkg-buildpackage: info: source package libvcflib dpkg-buildpackage: info: source version 1.0.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -699,7 +734,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/libvcflib-1.0.2+dfsg' dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/libvcflib-1.0.2+dfsg -B/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -714,19 +749,19 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o +[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o +[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o [ 2%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o -[ 3%] Building C object CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o -[ 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/Variant.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/Variant.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/rnglib.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/rnglib.cpp +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o +[ 4%] Building C object CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o +[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o +[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.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/var.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/var.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/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/cdflib.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/cdflib.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 +/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 +/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/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 [ 5%] Linking CXX shared library libvcflib.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vcflib.dir/link.txt --verbose=1 @@ -744,228 +779,236 @@ make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake --color= +make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend +make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsample2info.dir/DependInfo.cmake --color= +make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend +make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfevenregions.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-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake --color= +make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake --color= +make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfglbound.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfglbound.dir/depend.internal". 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vcfsitesummarize -make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build -[ 6%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -Scanning dependencies of target vcfroc make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +Scanning dependencies of target vcfremap make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build +Scanning dependencies of target vcfstreamsort make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build -[ 6%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build -make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build +Scanning dependencies of target vcfsample2info make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build -[ 6%] 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/vcfqual2info.dir/src/vcfqual2info.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfqual2info.cpp +make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -/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 +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfroc.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfroc.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfleftalign.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfleftalign.dir/depend.internal". +make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build +Scanning dependencies of target vcfroc +Scanning dependencies of target vcfleftalign +[ 5%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o +[ 7%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o +[ 7%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 8%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 9%] 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/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgeno2alleles.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/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfinfo2qual.cpp -[ 7%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -[ 8%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -[ 9%] 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 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CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend -[ 10%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -[ 11%] 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/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgeno2alleles.cpp -[ 11%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o +[ 9%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o +[ 9%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.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 +[ 10%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o +[ 10%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o /usr/bin/c++ 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-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/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build +[ 11%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.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 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CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build +/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 +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +/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 +/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 +[ 12%] 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/vcfsample2info.dir/src/vcfsample2info.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfsample2info.cpp [ 12%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o +[ 12%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o +[ 12%] 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/vcfremap.dir/src/vcfremap.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfremap.cpp +[ 13%] 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/vcfleftalign.dir/src/vcfleftalign.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfleftalign.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/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfstreamsort.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/vcfroc.dir/src/vcfroc.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfroc.cpp +[ 14%] 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-x86_64-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-x86_64-linux-gnu' +[ 14%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 14%] Built target vcfinfo2qual +make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcf2tsv.dir/DependInfo.cmake --color= +[ 15%] Linking CXX executable vcfsitesummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcf2tsv.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcf2tsv.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcf2tsv.dir/depend.internal". Scanning dependencies of 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/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build -[ 13%] 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]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 14%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o +[ 15%] Linking CXX executable vcfgenosamplenames +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 +[ 16%] 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 -[ 15%] 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-x86_64-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 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/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' [ 16%] Linking CXX executable vcfgeno2alleles /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 -[ 16%] Linking CXX executable vcfgenosamplenames -/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-x86_64-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/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/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-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-x86_64-linux-gnu' -[ 16%] Built target vcfinfo2qual +[ 16%] Built target vcfqual2info make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake --color= +[ 16%] Built target vcfsitesummarize +make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhethomratio.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhethomratio.dir/depend.internal". Scanning dependencies of target vcfhethomratio make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 17%] 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 -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 17%] Linking CXX executable vcfqual2info -[ 17%] Built target vcfglbound -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfqual2info.dir/link.txt --verbose=1 -make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake --color= -[ 17%] Built target vcfgeno2alleles -make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.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/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/meltEHH.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/meltEHH.dir/depend.internal". Scanning dependencies of target meltEHH make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 17%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +/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 +[ 18%] 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 +[ 18%] Built target vcfgenosamplenames +make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/depend.internal". -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' Scanning dependencies of target vcfallelicprimitives +[ 19%] Linking CXX executable vcfglbound make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglbound.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 18%] 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 -[ 19%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.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/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 20%] 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 -[ 19%] Built target vcfgenosamplenames +[ 20%] 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-x86_64-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-x86_64-linux-gnu' +[ 20%] Built target vcfgeno2alleles make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfuniq.dir/DependInfo.cmake --color= @@ -975,45 +1018,39 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 20%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 21%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 21%] Built target vcfqual2info +[ 21%] Built target vcfglbound make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhetcount.dir/DependInfo.cmake --color= +[ 21%] Linking CXX executable vcfsample2info +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhetcount.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhetcount.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfhetcount.dir/depend.internal". Scanning dependencies of target vcfhetcount make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' [ 22%] 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 -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 22%] Built target vcfsitesummarize +[ 22%] Built target vcfevenregions make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake --color= -[ 22%] Linking CXX executable vcfevenregions -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcommonsamples.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcommonsamples.dir/depend.internal". Scanning dependencies of target vcfcommonsamples make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build -/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-x86_64-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-x86_64-linux-gnu' [ 23%] 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 -[ 23%] 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-x86_64-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-x86_64-linux-gnu' -[ 23%] Built target vcfevenregions +[ 23%] Built target vcfsample2info make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake --color= @@ -1025,11 +1062,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 24%] 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/vcfindex.dir/src/vcfindex.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfindex.cpp -[ 25%] Linking CXX executable vcfbreakmulti -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 +[ 24%] Linking CXX executable vcf2dag +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.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-x86_64-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-x86_64-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/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 25%] Built target vcfsample2info +[ 24%] Built target vcf2dag make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake --color= @@ -1039,13 +1076,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 26%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -[ 27%] Linking CXX executable vcf2tsv +[ 25%] 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 -/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-x86_64-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 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-x86_64-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-x86_64-linux-gnu' -[ 27%] Built target vcfbreakmulti +[ 26%] Built target vcfbreakmulti make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/abba-baba.dir/DependInfo.cmake --color= @@ -1055,45 +1092,51 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 27%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o +[ 26%] 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 -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 27%] Built target vcf2tsv -make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/depend.internal". -Scanning dependencies of target vcfuniqalleles -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 28%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.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 -[ 28%] Linking CXX executable vcfuniq +[ 27%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 27%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 28%] Linking CXX executable vcfstreamsort +/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-x86_64-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-x86_64-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 28%] Built target vcfremap +make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend [ 28%] Built target vcfuniq +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake --color= make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfld.dir/DependInfo.cmake --color= -[ 28%] Linking CXX executable permuteGPAT++ -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfld.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfld.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfld.dir/depend.internal". -/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-x86_64-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 vcfld make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/build +[ 28%] Linking CXX executable vcfhethomratio +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/depend.internal". +Scanning dependencies of target vcfuniqalleles +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build +/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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 28%] Linking CXX executable permuteGPAT++ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 [ 29%] 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 -[ 30%] Linking CXX executable vcfstreamsort -/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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 30%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.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/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +/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 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 30%] Built target permuteGPAT++ +[ 30%] Built target vcfstreamsort make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake --color= @@ -1104,153 +1147,156 @@ make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 31%] 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 -[ 32%] 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-x86_64-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 vcfcombine +[ 31%] Linking CXX executable vcfcombine /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 +/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++ -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-x86_64-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-x86_64-linux-gnu' -[ 32%] Built target vcfstreamsort +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 31%] Built target permuteGPAT++ make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/plotHaps.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/plotHaps.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/plotHaps.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/plotHaps.dir/depend.internal". -Scanning dependencies of target plotHaps -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 33%] 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 -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 33%] Built target vcfremap +[ 31%] Built target vcfhethomratio make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentFst.dir/DependInfo.cmake --color= -[ 34%] Linking CXX executable vcfleftalign Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentFst.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentFst.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentFst.dir/depend.internal". Scanning dependencies of target segmentFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/build -/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-x86_64-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-x86_64-linux-gnu' -[ 34%] Building CXX object CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/plotHaps.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/plotHaps.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/plotHaps.dir/depend.internal". +[ 31%] Building CXX object CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o +Scanning dependencies of target plotHaps /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 -[ 35%] Linking CXX executable vcfcommonsamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 35%] Built target vcfcombine +make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 32%] 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 +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 32%] Built target vcfcombine make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffixup.dir/DependInfo.cmake --color= -[ 35%] Linking CXX executable vcfhetcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffixup.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffixup.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffixup.dir/depend.internal". Scanning dependencies of target vcffixup make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 35%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o +[ 32%] Linking CXX executable vcfhetcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 +[ 33%] Linking CXX executable vcf2tsv +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 +[ 33%] 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 -[ 35%] Linking CXX executable vcfhethomratio -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 +[ 34%] 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/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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 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/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 36%] Linking CXX executable vcfindex +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.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-x86_64-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-x86_64-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/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 35%] Built target vcfcommonsamples +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 36%] Built target vcf2tsv make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pVst.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pVst.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pVst.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pVst.dir/depend.internal". -Scanning dependencies of target pVst -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/build -[ 35%] Built target vcfleftalign -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 36%] Built target vcfhetcount make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake --color= -[ 35%] 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]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcheck.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcheck.dir/depend.internal". Scanning dependencies of target vcfcheck make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 35%] Built target vcfhetcount +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pVst.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pVst.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pVst.dir/depend.internal". +Scanning dependencies of target pVst +[ 36%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +/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 +make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 36%] 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 +[ 36%] Built target vcfleftalign make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend +[ 36%] Built target vcfcommonsamples make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfaltcount.dir/DependInfo.cmake --color= -[ 35%] 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 +make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfaltcount.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfaltcount.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfaltcount.dir/depend.internal". Scanning dependencies of target vcfaltcount make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 36%] 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 -[ 36%] Built target vcfhethomratio -make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake --color= -[ 37%] Linking CXX executable vcfindex -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/depend.internal". -/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-x86_64-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 dumpContigsFromHeader make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 37%] 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 +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 37%] 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 -[ 37%] Linking CXX executable vcf2dag -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 -[ 37%] Linking CXX executable vcfuniqalleles -/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-x86_64-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/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-x86_64-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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 37%] Built target vcfindex make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pFst.dir/DependInfo.cmake --color= -[ 37%] Built target vcfuniqalleles -make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/popStats.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pFst.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pFst.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/pFst.dir/depend.internal". Scanning dependencies of target pFst make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 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 +[ 38%] 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-x86_64-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-x86_64-linux-gnu' +[ 38%] Built target segmentFst +make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/popStats.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/popStats.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/popStats.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/popStats.dir/depend.internal". Scanning dependencies of target popStats -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 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 -[ 38%] Building CXX object CMakeFiles/popStats.dir/src/popStats.cpp.o +[ 39%] 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 -[ 38%] Built target vcf2dag +[ 39%] 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-x86_64-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 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 41%] 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-x86_64-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-x86_64-linux-gnu' +[ 41%] Built target vcfuniqalleles make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color= @@ -1260,13 +1306,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 39%] Linking CXX executable segmentFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.dir/link.txt --verbose=1 -[ 39%] 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 -/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-x86_64-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-x86_64-linux-gnu' -[ 39%] Built target segmentFst +[ 41%] 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 +[ 41%] Built target dumpContigsFromHeader make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake --color= @@ -1276,48 +1319,48 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 40%] Building CXX object CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o +[ 42%] 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 -[ 41%] 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-x86_64-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-x86_64-linux-gnu' -[ 42%] Linking CXX executable abba-baba -/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 [ 42%] Built target meltEHH make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfannotategenotypes.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/abba-baba.dir/src/abba-baba.cpp.o -o abba-baba -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 43%] Linking CXX executable abba-baba +/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/depend.internal". Scanning dependencies of target vcfannotategenotypes make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/abba-baba.dir/src/abba-baba.cpp.o -o abba-baba -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 43%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o +[ 44%] 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 -[ 44%] 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-x86_64-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 vcfcheck +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 44%] Built target abba-baba +/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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 45%] Built target abba-baba make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend +[ 45%] Linking CXX executable vcfroc +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/bFst.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/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu/CMakeFiles/bFst.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/bFst.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/bFst.dir/depend.internal". Scanning dependencies of target bFst make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 44%] Building CXX object CMakeFiles/bFst.dir/src/bFst.cpp.o +[ 45%] 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 -[ 45%] Linking CXX executable vcfcheck -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1 +[ 45%] Linking CXX executable vcfaltcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 45%] Built target dumpContigsFromHeader +/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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 45%] Built target vcfcheck make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/normalize-iHS.dir/DependInfo.cmake --color= @@ -1330,7 +1373,7 @@ [ 45%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 45%] Built target vcfcheck +[ 45%] Built target vcfroc make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/sequenceDiversity.dir/DependInfo.cmake --color= @@ -1340,21 +1383,26 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 45%] Building CXX object CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.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/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/sequenceDiversity.cpp -[ 45%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 45%] Built target vcfaltcount +make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentIhs.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentIhs.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentIhs.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentIhs.dir/depend.internal". +Scanning dependencies of target segmentIhs +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 45%] 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 [ 46%] Linking CXX executable vcffixup /usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.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/vcffixup.dir/src/vcffixup.cpp.o -o vcffixup -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 46%] Built target vcffixup -make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentIhs.dir/DependInfo.cmake --color= -[ 46%] Built target vcfaltcount make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/hapLrt.dir/DependInfo.cmake --color= @@ -1364,27 +1412,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentIhs.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentIhs.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/segmentIhs.dir/depend.internal". -Scanning dependencies of target segmentIhs [ 47%] 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-x86_64-linux-gnu' -make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 47%] 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 -[ 47%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 47%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 48%] Linking CXX executable normalize-iHS /usr/bin/cmake -E cmake_link_script CMakeFiles/normalize-iHS.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/normalize-iHS.dir/src/normalize-iHS.cpp.o -o normalize-iHS -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 48%] Built target vcf2fasta +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 48%] Built target normalize-iHS make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/wcFst.dir/DependInfo.cmake --color= @@ -1396,46 +1430,52 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 49%] 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 -O3 -fopenmp -o CMakeFiles/wcFst.dir/src/wcFst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/wcFst.cpp +[ 50%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 50%] 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-x86_64-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-x86_64-linux-gnu' -[ 49%] Built target plotHaps +[ 50%] Built target segmentIhs make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffilter.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffilter.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffilter.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcffilter.dir/depend.internal". Scanning dependencies of target vcffilter +[ 50%] Linking CXX executable plotHaps make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 49%] Built target normalize-iHS +/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 +[ 51%] 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 +/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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 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-x86_64-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-x86_64-linux-gnu' +[ 52%] Built target vcf2fasta make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake --color= -[ 50%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfrandom.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfrandom.dir/depend.internal". Scanning dependencies of target vcfrandom -/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 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 51%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o +[ 53%] 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 -[ 52%] 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-x86_64-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 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-x86_64-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 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-x86_64-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-x86_64-linux-gnu' -[ 54%] Built target segmentIhs +[ 54%] Linking CXX executable pFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 +[ 54%] Built target plotHaps make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/permuteSmooth.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/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu/CMakeFiles/permuteSmooth.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/permuteSmooth.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/permuteSmooth.dir/depend.internal". Scanning dependencies of target permuteSmooth @@ -1444,56 +1484,56 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 55%] 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 +[ 56%] 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-x86_64-linux-gnu' -[ 56%] Linking CXX executable vcfrandomsample -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 -[ 56%] Built target vcfcreatemulti +/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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 56%] Built target vcfld make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/genotypeSummary.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/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu/CMakeFiles/genotypeSummary.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/genotypeSummary.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/genotypeSummary.dir/depend.internal". -[ 57%] Linking CXX executable popStats Scanning dependencies of target genotypeSummary -/usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/build -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/popStats.dir/src/popStats.cpp.o -o popStats -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 57%] Built target vcfld -[ 58%] Building CXX object CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/depend +[ 57%] 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 +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 57%] Built target pVst +make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfecho.dir/DependInfo.cmake --color= +[ 57%] Built target pFst +make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfecho.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfecho.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfecho.dir/depend.internal". Scanning dependencies of target vcfecho make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 59%] 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 -[ 60%] 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-x86_64-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-x86_64-linux-gnu' -[ 60%] Built target popStats -make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfclassify.dir/DependInfo.cmake --color= +make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfclassify.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfclassify.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfclassify.dir/depend.internal". Scanning dependencies of target vcfclassify make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 58%] 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 +[ 59%] 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 +[ 60%] 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-x86_64-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 popStats +/usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.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/popStats.dir/src/popStats.cpp.o -o popStats -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' -[ 61%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o [ 61%] Built target vcfrandomsample -/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 make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake --color= @@ -1506,7 +1546,7 @@ [ 61%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 61%] Built target pFst +[ 61%] Built target popStats make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfentropy.dir/DependInfo.cmake --color= @@ -1518,14 +1558,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 62%] 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 -[ 62%] Linking CXX executable permuteSmooth -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 -[ 63%] 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/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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 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-x86_64-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-x86_64-linux-gnu' -[ 63%] Built target permuteSmooth +[ 62%] Built target vcfallelicprimitives make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake --color= @@ -1535,10 +1572,19 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 64%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o +[ 63%] 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 -[ 64%] Built target bFst +[ 64%] Linking CXX executable bFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 +[ 64%] 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/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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 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-x86_64-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-x86_64-linux-gnu' +[ 65%] Built target bFst make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake --color= @@ -1548,13 +1594,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 65%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.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/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfsamplenames.cpp -[ 65%] 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-x86_64-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-x86_64-linux-gnu' -[ 65%] Built target vcfecho +[ 66%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.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/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfsamplenames.cpp +[ 66%] Built target permuteSmooth make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake --color= @@ -1564,16 +1607,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 65%] 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 -[ 65%] 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-x86_64-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 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-x86_64-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-x86_64-linux-gnu' -[ 65%] Built target vcfclassify +[ 66%] 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 +[ 66%] Built target vcfcreatemulti make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color= @@ -1583,19 +1620,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 65%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o +[ 66%] Linking CXX executable vcfecho +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1 +[ 66%] 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/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgenotypecompare.cpp -[ 66%] 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-x86_64-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 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-x86_64-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 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/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-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/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 66%] Built target vcfallelicprimitives +[ 66%] Built target vcfecho make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake --color= @@ -1607,56 +1638,62 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 67%] 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 -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 +[ 68%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 68%] 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-x86_64-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-x86_64-linux-gnu' -[ 67%] Built target vcfremovesamples +[ 68%] Built target vcfremovesamples make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplediff.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplediff.dir/depend.internal". Scanning dependencies of target vcfsamplediff make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build -[ 67%] Built target vcfentropy -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 69%] Linking CXX executable sequenceDiversity +/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 68%] Linking CXX executable pVst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 -make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend -[ 69%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 70%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.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/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfsamplediff.cpp +[ 70%] Built target vcfclassify +make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake --color= -[ 69%] Built target vcfrandom -/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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/depend.internal". Scanning dependencies of target vcfremoveaberrantgenotypes make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/depend.internal". make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 70%] Linking CXX executable vcfsamplenames +[ 70%] 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 +[ 70%] 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-x86_64-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-x86_64-linux-gnu' +[ 70%] Built target sequenceDiversity +make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color= +[ 71%] Linking CXX executable vcfsamplenames /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/depend.internal". Scanning dependencies of target vcfparsealts make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 70%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -[ 70%] 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/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfremoveaberrantgenotypes.cpp +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 71%] 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 -[ 71%] 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-x86_64-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-x86_64-linux-gnu' -[ 71%] Built target vcfsamplenames +[ 71%] Built target vcfrandom make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfafpath.dir/DependInfo.cmake --color= @@ -1665,59 +1702,59 @@ Scanning dependencies of target vcfafpath make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 71%] Linking CXX executable hapLrt -/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 71%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -[ 71%] Built target pVst /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 +[ 72%] Linking CXX executable wcFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 72%] 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/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 72%] Built target vcfsamplenames make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfstats.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfstats.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfstats.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfstats.dir/depend.internal". -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' Scanning dependencies of target vcfstats make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 71%] Built target sequenceDiversity +[ 72%] 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 +[ 72%] 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-x86_64-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-x86_64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 72%] Built target vcfkeepsamples make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake --color= -[ 71%] 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 +[ 72%] Built target wcFst +make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfflatten.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfflatten.dir/depend.internal". Scanning dependencies of target vcfflatten make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 71%] 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 -[ 71%] Built target hapLrt -make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfprimers.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfprimers.dir/depend.internal". Scanning dependencies of target vcfprimers make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build -[ 71%] Linking CXX executable vcfkeepsamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 72%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o +[ 73%] 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 -[ 73%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 73%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 73%] Built target vcfkeepsamples +[ 73%] Built target vcfentropy make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/iHS.dir/DependInfo.cmake --color= @@ -1729,28 +1766,25 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 74%] 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 +[ 74%] Linking CXX executable hapLrt +/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-x86_64-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-x86_64-linux-gnu' -[ 74%] Built target vcfannotategenotypes +[ 74%] Built target hapLrt make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend +[ 75%] Linking CXX executable vcffilter +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfnumalt.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat 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Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfnumalt.dir/depend.internal". Scanning dependencies of target vcfnumalt make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 74%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o +[ 75%] 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 -[ 75%] 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-x86_64-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 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-x86_64-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 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/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' [ 75%] Built target vcffilter make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend @@ -1764,25 +1798,30 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' [ 75%] 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 -[ 76%] 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-x86_64-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 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-x86_64-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 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-x86_64-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-x86_64-linux-gnu' -[ 76%] Built target vcfroc +[ 76%] Built target genotypeSummary make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 77%] Linking CXX executable vcfinfosummarize Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcountalleles.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcountalleles.dir/depend.internal". -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfosummarize.dir/link.txt --verbose=1 Scanning dependencies of target vcfcountalleles make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 77%] Built target genotypeSummary -/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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 76%] 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 +[ 77%] 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-x86_64-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-x86_64-linux-gnu' +[ 77%] Built target vcfinfosummarize make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcat.dir/DependInfo.cmake --color= @@ -1791,90 +1830,91 @@ Scanning dependencies of target vcfcat make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build -[ 77%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -/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 +[ 77%] 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 [ 78%] Linking CXX executable vcfparsealts /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 -[ 78%] 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 -/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-x86_64-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-x86_64-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 78%] Built target vcfparsealts -[ 78%] Built target wcFst +/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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 78%] Built target vcfremoveaberrantgenotypes make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/depend.internal". +Scanning dependencies of target vcfcleancomplex +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 79%] 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 +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 79%] Built target vcfparsealts make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/smoother.dir/DependInfo.cmake --color= -[ 78%] Built target vcfinfosummarize -make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfintersect.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/smoother.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/smoother.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/smoother.dir/depend.internal". Scanning dependencies of target smoother -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/depend.internal". -Scanning dependencies of target vcfcleancomplex make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 80%] 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 +[ 80%] Linking CXX executable vcfprimers +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 +[ 81%] 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/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -o vcfannotategenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' +[ 81%] Built target vcfannotategenotypes +make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build +cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfintersect.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfintersect.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfintersect.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfintersect.dir/depend.internal". -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' Scanning dependencies of target vcfintersect make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build +[ 81%] Built target vcfprimers make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 79%] 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 -[ 80%] 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 -[ 80%] 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 -[ 80%] Linking CXX executable vcfsamplediff -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.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/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 81%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder 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Scanning dependencies of target vcfannotate make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 81%] Built target vcfremoveaberrantgenotypes make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build -make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 82%] 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 +[ 83%] Linking CXX executable vcfafpath +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1 +[ 83%] Linking CXX executable vcfsamplediff +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.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-x86_64-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/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' +[ 83%] Built target vcfsamplediff +make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfoverlay.dir/DependInfo.cmake --color= -[ 82%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfoverlay.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfoverlay.dir/depend.internal". 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Scanning dependencies of target vcfoverlay make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/build -/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 -[ 82%] Linking CXX executable vcfprimers -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 82%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o +[ 83%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.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/vcfoverlay.dir/src/vcfoverlay.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfoverlay.cpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 82%] Built target vcfprimers +[ 83%] Built target vcfafpath make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake --color= @@ -1884,36 +1924,30 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 82%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o +[ 83%] 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 -[ 83%] Linking CXX executable vcfcountalleles +[ 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 85%] 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 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Scanning dependencies of target vcfkeepinfo make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 84%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o +[ 86%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 85%] Linking CXX executable vcfcat -[ 86%] Linking CXX executable vcfnumalt -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 -/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/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 86%] Built target smoother +[ 86%] Built target vcfcountalleles make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.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/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/depend.internal". @@ -1922,10 +1956,16 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 87%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o +[ 87%] Linking CXX executable vcfgenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 +[ 88%] 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/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgenosummarize.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/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 89%] 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-x86_64-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-x86_64-linux-gnu' -[ 87%] Built target vcfcat +[ 89%] Built target vcfcat make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake --color= @@ -1935,14 +1975,11 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 88%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o +[ 90%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.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/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfkeepgeno.cpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 89%] Linking CXX executable vcfgenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 -[ 89%] Built target vcfnumalt +[ 90%] Built target vcfgenotypes make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.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/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfdistance.dir/depend.internal". @@ -1951,107 +1988,105 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 89%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o +[ 90%] 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 +[ 90%] Linking CXX executable smoother +/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 +[ 91%] 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/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu' -[ 89%] Built target vcfgenotypes +[ 91%] Built target smoother make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake --color= +[ 91%] Linking CXX executable vcfcleancomplex +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcflength.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcflength.dir/depend.internal". Scanning dependencies of target vcflength make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build +/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-x86_64-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-x86_64-linux-gnu' -[ 89%] 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 /build/libvcflib-1.0.2+dfsg/src/vcflength.cpp -[ 89%] Linking CXX executable vcfcleancomplex -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 -[ 90%] 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/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -o vcfcleancomplex -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-x86_64-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 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-x86_64-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-x86_64-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target vcfcleancomplex +[ 91%] Built target vcfflatten make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake --color= -[ 91%] Built target vcfafpath Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfglxgt.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/vcfglxgt.dir/depend.internal". +[ 92%] Linking CXX executable vcfgenotypecompare +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 Scanning dependencies of target vcfglxgt make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build +/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-x86_64-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-x86_64-linux-gnu' -[ 92%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o +[ 93%] 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 -[ 93%] Linking CXX executable vcfaddinfo -/usr/bin/cmake -E cmake_link_script 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directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' +[ 94%] Built target vcfaddinfo +[ 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 95%] 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=. -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-x86_64-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-x86_64-linux-gnu' +[ 95%] Built target vcfstats make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 94%] Built target vcfgenotypecompare -[ 94%] Built target iHS -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 94%] Built target vcfkeepinfo -[ 94%] Linking CXX executable vcfkeepgeno +[ 95%] Built target vcfkeepinfo +[ 95%] Linking CXX executable vcfkeepgeno /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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-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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 96%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 96%] 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-x86_64-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-x86_64-linux-gnu' -[ 96%] Built target vcfdistance +[ 96%] Built target vcfkeepgeno make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 96%] Built target vcflength -[ 97%] Linking CXX executable vcfstats -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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-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-x86_64-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-x86_64-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 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-x86_64-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-x86_64-linux-gnu' [ 98%] Built target vcfgenosummarize make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target vcfgeno2haplo -[ 98%] 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-x86_64-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-x86_64-linux-gnu' -[ 98%] Built target vcfglxgt +[ 98%] Built target vcflength [ 99%] 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-x86_64-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-x86_64-linux-gnu' [ 99%] Built target vcfoverlay +[ 99%] 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-x86_64-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-x86_64-linux-gnu' +[ 99%] Built target vcfglxgt [ 99%] 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-x86_64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp @@ -2077,22 +2112,22 @@ [----------] Global test environment set-up. [----------] 1 test from Variant [ RUN ] Variant.correctGenotype -[ OK ] Variant.correctGenotype (3114 ms) -[----------] 1 test from Variant (3114 ms total) +[ OK ] Variant.correctGenotype (2764 ms) +[----------] 1 test from Variant (2764 ms total) [----------] 4 tests from VariantCallFile [ RUN ] VariantCallFile.open -[ OK ] VariantCallFile.open (1 ms) +[ OK ] VariantCallFile.open (0 ms) [ RUN ] VariantCallFile.recordCountUncompressed [ OK ] VariantCallFile.recordCountUncompressed (0 ms) [ RUN ] VariantCallFile.recordCountCompressed [ OK ] VariantCallFile.recordCountCompressed (5 ms) [ RUN ] VariantCallFile.sampleNamesCompressed [ OK ] VariantCallFile.sampleNamesCompressed (2 ms) -[----------] 4 tests from VariantCallFile (8 ms total) +[----------] 4 tests from VariantCallFile (7 ms total) [----------] Global test environment tear-down -[==========] 5 tests from 2 test suites ran. (3123 ms total) +[==========] 5 tests from 2 test suites ran. (2771 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' @@ -2100,7 +2135,7 @@ dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake - cd obj-x86_64-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-x86_64-linux-gnu && make -j15 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-x86_64-linux-gnu' /usr/bin/cmake -S/build/libvcflib-1.0.2+dfsg -B/build/libvcflib-1.0.2+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2424,8 +2459,8 @@ dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.2+dfsg-2_amd64.deb'. -dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.2+dfsg-2_amd64.deb'. +dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.2+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary @@ -2435,12 +2470,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/480769/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/480769/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/3605696 and its subdirectories -I: Current time: Tue Jan 31 11:11:05 -12 2023 -I: pbuilder-time-stamp: 1675206665 +I: removing directory /srv/workspace/pbuilder/480769 and its subdirectories +I: Current time: Thu Dec 30 06:50:10 +14 2021 +I: pbuilder-time-stamp: 1640796610