Diff of the two buildlogs: -- --- b1/build.log 2021-08-14 05:24:17.271757577 +0000 +++ b2/build.log 2021-08-14 05:29:35.255844838 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Aug 13 17:13:42 -12 2021 -I: pbuilder-time-stamp: 1628918022 +I: Current time: Sat Sep 17 01:47:20 +14 2022 +I: pbuilder-time-stamp: 1663328840 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.5gSX2uH9/trustedkeys.kbx': General error -gpgv: Signature made Thu Jan 28 00:04:01 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.X07Qi5_T/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/17037/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13896/tmp/hooks/D01_modify_environment starting +debug: Running on codethink11-arm64. +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/13896/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13896/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='17037' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=13896 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.4IRo0r0Xkz/pbuilderrc_qZZ7 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4IRo0r0Xkz/b1 --logfile b1/build.log libvcflib_1.0.2+dfsg-2.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.4IRo0r0Xkz/pbuilderrc_leBb --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.4IRo0r0Xkz/b2 --logfile b2/build.log --extrapackages usrmerge libvcflib_1.0.2+dfsg-2.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink14-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Jul 28 07:09 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 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jul 28 07:09 more - -rwsr-xr-x 1 root root 51360 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 14496 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 11 21:25 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jul 28 07:09 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/17037/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Aug 5 2021 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Jul 29 2021 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 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Jul 29 2021 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 178400 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 93744 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Jul 29 2021 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jul 29 2021 more + -rwsr-xr-x 1 root root 51360 Jul 29 2021 mount + -rwxr-xr-x 1 root root 14496 Jul 29 2021 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 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 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 17 01:47 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 15 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jul 29 2021 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jul 29 2021 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Jul 29 2021 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/13896/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 arm64 libtabixpp-dev arm64 1.1.0-4 [8108 B] Get: 73 http://deb.debian.org/debian bullseye/main arm64 markdown all 1.0.1-10.1 [17.5 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] -Fetched 33.9 MB in 4s (8326 kB/s) +Fetched 33.9 MB in 1s (49.8 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 ... 19646 files and directories currently installed.) @@ -607,8 +641,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (864 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25255 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/libvcflib-1.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && 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: Temporary failure in name resolution +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 @@ -714,19 +785,19 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/Variant.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/Variant.cpp -[ 2%] 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 +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o [ 2%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o +[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o [ 3%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/Variant.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/Variant.cpp +[ 4%] Building C object CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/rnglib.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/rnglib.cpp -[ 3%] 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/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 -[ 4%] Building C object CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o /usr/bin/cc -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -c /build/libvcflib-1.0.2+dfsg/filevercmp/filevercmp.c [ 5%] Linking CXX shared library libvcflib.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vcflib.dir/link.txt --verbose=1 @@ -735,99 +806,96 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 5%] Built target vcflib make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend +make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend +make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend +make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend +make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend +make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend +make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend -make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend +make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsample2info.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2alleles.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-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfglbound.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake" is newer than depender 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'/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build Scanning dependencies of target vcfgenosamplenames -Scanning dependencies of target vcfcombine +Scanning dependencies of target vcf2dag make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build -Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/depend.internal". make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build -[ 6%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -[ 6%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -Scanning dependencies of target vcfgeno2alleles -/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 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CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o +[ 8%] 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/vcfsample2info.dir/src/vcfsample2info.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfsample2info.cpp -[ 11%] 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 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CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgenosamplenames.cpp +[ 11%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.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 [ 12%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 12%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 12%] Linking CXX executable vcfgeno2alleles /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp @@ -836,29 +904,35 @@ make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfevenregions.dir/DependInfo.cmake --color= +[ 12%] Linking CXX executable vcfqual2info Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfevenregions.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfevenregions.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfevenregions.dir/depend.internal". +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfqual2info.dir/link.txt --verbose=1 Scanning dependencies of target vcfevenregions make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-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/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 13%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfevenregions.cpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 13%] Built target vcfqual2info +[ 13%] Built target vcfgeno2alleles make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= +[ 13%] Linking CXX executable vcfgenosamplenames +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/depend.internal". Scanning dependencies of target vcfbreakmulti make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-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/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 13%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfbreakmulti.cpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 13%] Built target vcfgeno2alleles +[ 13%] Built target vcfqual2info make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake --color= @@ -870,9 +944,6 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 13%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfsitesummarize.cpp -[ 13%] Linking CXX executable vcfgenosamplenames -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 14%] Linking CXX executable 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/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp @@ -934,12 +1005,12 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 15%] 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 +[ 15%] 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-aarch64-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 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-aarch64-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 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-aarch64-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-aarch64-linux-gnu' [ 16%] Built target vcfevenregions make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend @@ -1014,14 +1085,14 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 23%] 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 -[ 23%] Linking CXX executable vcfhethomratio -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 24%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 24%] Linking CXX executable vcfhethomratio +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' -[ 24%] Built target vcfhethomratio +[ 24%] Built target vcfstreamsort make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfhetcount.dir/DependInfo.cmake --color= @@ -1034,7 +1105,7 @@ [ 25%] 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-aarch64-linux-gnu' -[ 25%] Built target vcfstreamsort +[ 25%] Built target vcfhethomratio make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake --color= @@ -1050,7 +1121,10 @@ /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-aarch64-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-aarch64-linux-gnu' -[ 27%] Built target vcf2tsv +[ 28%] Linking CXX executable vcfleftalign +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 28%] Built target vcf2tsv make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake --color= @@ -1060,11 +1134,8 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 28%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o +[ 29%] 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 -[ 29%] Linking CXX executable vcfleftalign -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' [ 29%] Built target vcfleftalign make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend @@ -1081,9 +1152,6 @@ [ 30%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 30%] Linking CXX executable permuteGPAT++ -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' [ 30%] Built target vcfuniq make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend @@ -1097,6 +1165,9 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 30%] 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 +[ 30%] Linking CXX executable permuteGPAT++ +/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' [ 30%] Built target permuteGPAT++ make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend @@ -1113,6 +1184,9 @@ [ 32%] Linking CXX executable vcfcommonsamples /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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 vcfhetcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' [ 32%] Built target vcfcommonsamples make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/depend @@ -1126,11 +1200,8 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 33%] 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 -[ 34%] 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-aarch64-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-aarch64-linux-gnu' -[ 34%] Built target vcfindex +[ 33%] Built target vcfhetcount make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake --color= @@ -1140,13 +1211,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 35%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o +[ 34%] 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 -[ 35%] Linking CXX executable vcfhetcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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 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-aarch64-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-aarch64-linux-gnu' -[ 35%] Built target vcfhetcount +[ 35%] Built target meltEHH make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/plotHaps.dir/DependInfo.cmake --color= @@ -1158,11 +1229,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 36%] 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 -[ 37%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 37%] Linking CXX executable 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-aarch64-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-aarch64-linux-gnu' -[ 37%] Built target meltEHH +[ 37%] Built target vcfindex make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/segmentFst.dir/DependInfo.cmake --color= @@ -1177,24 +1248,24 @@ [ 37%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 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-aarch64-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-aarch64-linux-gnu' -[ 38%] Built target vcfuniqalleles +[ 37%] Linking CXX executable vcfroc +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 +[ 37%] Built target vcfuniqalleles make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd 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"/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcffixup.dir/depend.internal". 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Scanning dependencies of target vcffixup make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 38%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o +[ 37%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 38%] Built target segmentFst +[ 37%] Built target vcfroc make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/pVst.dir/DependInfo.cmake --color= @@ -1204,13 +1275,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 38%] Building CXX object CMakeFiles/pVst.dir/src/pVst.cpp.o +[ 37%] 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 -[ 38%] 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 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38%] Built target segmentFst make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake --color= @@ -1240,44 +1311,41 @@ /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 [ 40%] Linking CXX executable vcf2fasta /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 +[ 41%] 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/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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 vcfcheck +/usr/bin/c++ -g -O2 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-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-aarch64-linux-gnu' -[ 41%] Built target vcf2fasta +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +[ 42%] Built target vcf2fasta make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 41%] Built target vcfcheck -Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/depend.internal". +[ 42%] Built target vcfld make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/depend -Scanning dependencies of target dumpContigsFromHeader make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/pFst.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/depend.internal". +Scanning dependencies of target dumpContigsFromHeader make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/pFst.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/pFst.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/pFst.dir/depend.internal". +make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build Scanning dependencies of target pFst make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 41%] Building CXX object CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o +[ 42%] 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 -[ 42%] Linking CXX executable vcfld -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 [ 42%] 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 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 42%] Linking CXX executable 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-aarch64-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-aarch64-linux-gnu' -[ 42%] Built target vcfld +[ 42%] Built target vcfcheck make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/popStats.dir/DependInfo.cmake --color= @@ -1289,40 +1357,46 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 43%] Building CXX object CMakeFiles/popStats.dir/src/popStats.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/popStats.dir/src/popStats.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/popStats.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 43%] Built target plotHaps -make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/depend.internal". -Scanning dependencies of target vcfcreatemulti -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 43%] 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 +[ 43%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 44%] 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-aarch64-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-aarch64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 44%] Built target vcffixup +[ 44%] Built target plotHaps +make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandomsample.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandomsample.dir/depend.internal". Scanning dependencies of target vcfrandomsample +Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/depend.internal". make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build +Scanning dependencies of target vcfcreatemulti +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build +[ 44%] Linking CXX executable vcfallelicprimitives +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-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/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -o vcfallelicprimitives -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 45%] 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 +[ 45%] 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 [ 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-aarch64-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-aarch64-linux-gnu' -[ 45%] Built target vcfaltcount +[ 45%] Built target vcfallelicprimitives make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake --color= @@ -1331,15 +1405,12 @@ Scanning dependencies of target vcfannotategenotypes make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +[ 45%] Built target vcfaltcount +make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend [ 46%] 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 -[ 46%] 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-aarch64-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-aarch64-linux-gnu' -[ 46%] Built target vcfallelicprimitives -make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/bFst.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/bFst.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/bFst.dir/depend.internal". @@ -1401,11 +1472,8 @@ [ 50%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 51%] Linking CXX executable 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-aarch64-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-aarch64-linux-gnu' -[ 51%] Built target vcfrandomsample +[ 50%] Built target vcfrandomsample make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/hapLrt.dir/DependInfo.cmake --color= @@ -1415,8 +1483,11 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +[ 51%] Linking CXX executable popStats +/usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1 [ 52%] 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 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-aarch64-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-aarch64-linux-gnu' [ 52%] Built target popStats make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend @@ -1440,33 +1511,33 @@ cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcffilter.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcffilter.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcffilter.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcffilter.dir/depend.internal". -[ 55%] Linking CXX executable segmentIhs Scanning dependencies of target vcffilter -/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.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/segmentIhs.dir/src/segmentIhs.cpp.o -o segmentIhs -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' +[ 55%] Linking CXX executable vcfcreatemulti +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 [ 56%] 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/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' -[ 56%] Built target segmentIhs +[ 56%] Built target vcfcreatemulti make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake --color= +[ 57%] Linking CXX executable segmentIhs +/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.dir/link.txt --verbose=1 Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandom.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandom.dir/depend.internal". Scanning dependencies of target vcfrandom make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 57%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o +[ 58%] 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 -[ 58%] 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-aarch64-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/segmentIhs.dir/src/segmentIhs.cpp.o -o segmentIhs -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' -[ 58%] Built target vcfcreatemulti +[ 58%] Built target segmentIhs make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/permuteSmooth.dir/DependInfo.cmake --color= @@ -1542,14 +1613,14 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 64%] 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 -[ 65%] Linking CXX executable wcFst +[ 65%] 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-aarch64-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 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-aarch64-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 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-aarch64-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-aarch64-linux-gnu' -[ 65%] Built target wcFst +[ 66%] Built target vcffilter make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfentropy.dir/DependInfo.cmake --color= @@ -1559,13 +1630,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 66%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o +[ 67%] 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 -[ 67%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 67%] Linking CXX executable vcfecho +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 67%] Built target vcfecho +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 67%] Built target wcFst make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake --color= @@ -1577,24 +1648,30 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 68%] 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 -[ 69%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 69%] 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-aarch64-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-aarch64-linux-gnu' -[ 69%] Built target vcfannotategenotypes +[ 69%] Built target vcfecho make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake --color= +[ 69%] 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-aarch64-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-aarch64-linux-gnu/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsamplenames.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsamplenames.dir/depend.internal". Scanning dependencies of target vcfsamplenames make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +[ 69%] Linking CXX executable hapLrt +/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.dir/link.txt --verbose=1 [ 70%] 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 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-aarch64-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-aarch64-linux-gnu' -[ 70%] Built target vcffilter +[ 70%] Built target vcfannotategenotypes make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake --color= @@ -1606,43 +1683,37 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 70%] 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 -[ 70%] 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-aarch64-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-aarch64-linux-gnu' -[ 70%] Built target hapLrt +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +[ 70%] Built target genotypeSummary make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color= +[ 70%] Built target hapLrt +make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/depend.internal". Scanning dependencies of target vcfgenotypecompare make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 70%] 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 -[ 70%] 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-aarch64-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-aarch64-linux-gnu' -[ 70%] Built target vcfclassify -make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/depend.internal". Scanning dependencies of target vcfgeno2haplo make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' +[ 70%] 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 [ 71%] 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 -[ 72%] Linking CXX executable vcfsamplenames -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 71%] 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-aarch64-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-aarch64-linux-gnu' -[ 72%] Built target vcfsamplenames +[ 71%] Built target vcfclassify make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake --color= @@ -1652,13 +1723,16 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 73%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o +[ 72%] 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 +[ 73%] Linking CXX executable vcfsamplenames +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 74%] 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-aarch64-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-aarch64-linux-gnu' -[ 74%] Built target vcfremovesamples +[ 74%] Built target vcfsamplenames make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake --color= @@ -1670,11 +1744,8 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 74%] 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 -[ 74%] 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-aarch64-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-aarch64-linux-gnu' -[ 74%] Built target genotypeSummary +[ 74%] Built target vcfremovesamples make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color= @@ -1758,17 +1829,17 @@ make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/iHS.dir/DependInfo.cmake --color= +[ 78%] Linking CXX executable vcfsamplediff Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/iHS.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/iHS.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/iHS.dir/depend.internal". +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.dir/link.txt --verbose=1 Scanning dependencies of target iHS make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-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/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 79%] 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 -[ 79%] 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-aarch64-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-aarch64-linux-gnu' [ 79%] Built target vcfsamplediff make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend @@ -1785,6 +1856,9 @@ [ 80%] Linking CXX executable vcfafpath /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 80%] Linking CXX executable vcfprimers +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.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-aarch64-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-aarch64-linux-gnu' [ 80%] Built target vcfafpath make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend @@ -1798,9 +1872,6 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 80%] 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 -[ 80%] Linking CXX executable vcfprimers -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.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-aarch64-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-aarch64-linux-gnu' [ 80%] Built target vcfprimers make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend @@ -1817,11 +1888,8 @@ [ 81%] Linking CXX executable vcfgenotypecompare /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 82%] Linking CXX executable 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-aarch64-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-aarch64-linux-gnu' -[ 82%] Built target vcfgenotypecompare +[ 81%] Built target vcfgenotypecompare make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcat.dir/DependInfo.cmake --color= @@ -1831,10 +1899,16 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 82%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o +[ 81%] 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 +[ 82%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 83%] Linking CXX executable 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-aarch64-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-aarch64-linux-gnu' -[ 82%] Built target vcfnumalt +[ 83%] Built target vcfnumalt make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake --color= @@ -1844,11 +1918,8 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 83%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o +[ 84%] 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 -[ 84%] 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-aarch64-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-aarch64-linux-gnu' [ 84%] Built target vcfflatten make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/depend @@ -1862,14 +1933,14 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 85%] 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 -[ 86%] Linking CXX executable vcfgenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 87%] Linking CXX executable vcfcountalleles +[ 86%] Linking CXX executable vcfcountalleles /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 86%] Linking CXX executable vcfgeno2haplo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -o vcfgeno2haplo -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' -[ 87%] Built target vcfgenotypes +[ 86%] Built target vcfcountalleles make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfintersect.dir/DependInfo.cmake --color= @@ -1879,10 +1950,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 87%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o +[ 86%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 87%] Built target vcfcountalleles +[ 86%] Built target vcfgeno2haplo make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfannotate.dir/DependInfo.cmake --color= @@ -1892,31 +1963,28 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 88%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o +[ 87%] 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 -[ 88%] Linking CXX executable vcfgeno2haplo -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -o vcfgeno2haplo -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 88%] Linking CXX executable vcfgenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-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-aarch64-linux-gnu' -[ 88%] Built target vcfgeno2haplo +[ 89%] Built target vcfgenotypes make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfoverlay.dir/DependInfo.cmake --color= -[ 89%] Linking CXX executable vcfcat Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfoverlay.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfoverlay.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfoverlay.dir/depend.internal". Scanning dependencies of target vcfoverlay make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/build -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-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/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 89%] 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-aarch64-linux-gnu' -[ 89%] Linking CXX executable iHS -/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 89%] Built target vcfcat make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' @@ -1929,14 +1997,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 89%] 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 -[ 89%] Linking CXX executable smoother -/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 [ 90%] Linking CXX executable vcfstats -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-aarch64-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/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-aarch64-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-aarch64-linux-gnu' -[ 90%] Built target iHS +[ 90%] Built target vcfstats make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake --color= @@ -1951,8 +2016,11 @@ [ 91%] Linking CXX executable vcfcleancomplex /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -o vcfcleancomplex -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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 smoother +/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' -[ 91%] Built target smoother +[ 91%] Built target vcfcleancomplex make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake --color= @@ -1965,10 +2033,13 @@ [ 92%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 92%] Built target vcfstats +[ 92%] Built target smoother make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend +[ 92%] Linking CXX executable iHS +/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepgeno.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/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/depend.internal". Scanning dependencies of target vcfkeepgeno @@ -1978,7 +2049,7 @@ [ 93%] 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-aarch64-linux-gnu' -[ 93%] Built target vcfcleancomplex +[ 93%] Built target iHS make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake --color= @@ -1990,14 +2061,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 93%] 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 -[ 93%] 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 94%] Linking CXX executable vcfaddinfo /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -o vcfaddinfo -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' -[ 94%] Built target vcfkeepinfo +[ 94%] Built target vcfaddinfo make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake --color= @@ -2009,8 +2077,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 94%] 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 +[ 94%] 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-aarch64-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-aarch64-linux-gnu' -[ 94%] Built target vcfaddinfo +[ 94%] Built target vcfkeepinfo make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake --color= @@ -2022,41 +2093,41 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 95%] 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 -[ 95%] Linking CXX executable vcfkeepgeno -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-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-aarch64-linux-gnu' -[ 96%] Built target vcfkeepgeno -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 96%] Built target vcfdistance +[ 96%] Linking CXX executable vcfkeepgeno +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 97%] Linking CXX executable vcfgenosummarize /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -o vcfgenosummarize -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-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-aarch64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' [ 97%] Built target vcfgenosummarize +[ 97%] Built target vcfkeepgeno [ 98%] 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-aarch64-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-aarch64-linux-gnu' [ 98%] Built target vcfoverlay -[ 98%] Linking CXX executable vcfannotate +[ 99%] 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-aarch64-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-aarch64-linux-gnu' +[ 99%] Built target vcflength +[ 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-aarch64-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-aarch64-linux-gnu' -[ 98%] Built target vcfannotate -[ 98%] Linking CXX executable vcfglxgt +[ 99%] Built target vcfannotate +[ 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-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 99%] 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-aarch64-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-aarch64-linux-gnu' [ 99%] Built target vcfglxgt -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu' -[ 99%] Built target vcflength [100%] Linking CXX executable vcfintersect /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-aarch64-linux-gnu: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp @@ -2077,8 +2148,8 @@ [----------] Global test environment set-up. [----------] 1 test from Variant [ RUN ] Variant.correctGenotype -[ OK ] Variant.correctGenotype (5394 ms) -[----------] 1 test from Variant (5394 ms total) +[ OK ] Variant.correctGenotype (5445 ms) +[----------] 1 test from Variant (5446 ms total) [----------] 4 tests from VariantCallFile [ RUN ] VariantCallFile.open @@ -2092,7 +2163,7 @@ [----------] 4 tests from VariantCallFile (12 ms total) [----------] Global test environment tear-down -[==========] 5 tests from 2 test suites ran. (5406 ms total) +[==========] 5 tests from 2 test suites ran. (5458 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' @@ -2423,11 +2494,11 @@ dh_gencontrol -O--buildsystem=cmake dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake +dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.2+dfsg-2_arm64.deb'. dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.2+dfsg-2_arm64.deb'. dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.2+dfsg-2_arm64.deb'. dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.2+dfsg-2_arm64.deb'. dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.2+dfsg-2_arm64.deb'. -dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.2+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libvcflib_1.0.2+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2435,12 +2506,14 @@ 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/13896/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13896/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/17037 and its subdirectories -I: Current time: Fri Aug 13 17:24:16 -12 2021 -I: pbuilder-time-stamp: 1628918656 +I: removing directory /srv/workspace/pbuilder/13896 and its subdirectories +I: Current time: Sat Sep 17 01:52:33 +14 2022 +I: pbuilder-time-stamp: 1663329153