Diff of the two buildlogs: -- --- b1/build.log 2021-07-21 10:57:10.128586885 +0000 +++ b2/build.log 2021-07-21 11:23:27.929503724 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jul 20 22:40:18 -12 2021 -I: pbuilder-time-stamp: 1626864018 +I: Current time: Thu Jul 22 00:57:45 +14 2021 +I: pbuilder-time-stamp: 1626865065 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.frZ87qZ5/trustedkeys.kbx': General error -gpgv: Signature made Thu Jan 28 00:04:01 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.3681Lc7L/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/12780/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/8964/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +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/8964/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/8964/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=5' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='f0bea588a3644b5ea88c999092514edb' - 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='12780' - PS1='# ' - PS2='> ' + INVOCATION_ID=50e684f1fc86405998c437057b8a52fc + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=8964 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.gLDK4MJTvC/pbuilderrc_6jdH --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.gLDK4MJTvC/b1 --logfile b1/build.log libvcflib_1.0.2+dfsg-2.dsc' - SUDO_GID='114' - SUDO_UID='109' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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.gLDK4MJTvC/pbuilderrc_KAj4 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.gLDK4MJTvC/b2 --logfile b2/build.log --extrapackages usrmerge libvcflib_1.0.2+dfsg-2.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux ff64a 5.10.0-7-arm64 #1 SMP Debian 5.10.40-1 (2021-05-28) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-7-armmp-lpae #1 SMP Debian 5.10.40-1 (2021-05-28) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Feb 7 02:38 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 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 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 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more - -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 88524 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 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 19 21:26 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Feb 7 02:38 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/12780/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Feb 8 04:38 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 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more + -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 22 00:58 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 18 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/8964/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 armhf libtabixpp-dev armhf 1.1.0-4 [8024 B] Get: 73 http://deb.debian.org/debian bullseye/main armhf markdown all 1.0.1-10.1 [17.5 kB] Get: 74 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] -Fetched 34.4 MB in 6s (5940 kB/s) +Fetched 34.4 MB in 5s (7055 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 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 armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (870 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 ... 25007 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: Name or service not known +I: Running cd /build/libvcflib-1.0.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libvcflib_1.0.2+dfsg-2_source.changes dpkg-buildpackage: info: source package libvcflib dpkg-buildpackage: info: source version 1.0.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -699,7 +770,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/libvcflib-1.0.2+dfsg' dh_auto_build - cd obj-arm-linux-gnueabihf && make -j5 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libvcflib-1.0.2+dfsg -B/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks @@ -714,18 +785,16 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o -[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o +[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/Variant.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/Variant.cpp -/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 +[ 1%] 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/rnglib.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/rnglib.cpp -[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/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 [ 3%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -o CMakeFiles/vcflib.dir/src/cdflib.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/cdflib.cpp -/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 -[ 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/split.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/split.cpp In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/var.hpp:17, from /build/libvcflib-1.0.2+dfsg/src/var.cpp:20: @@ -778,8 +847,8 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 4%] Building C object CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -/usr/bin/cc -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -c /build/libvcflib-1.0.2+dfsg/filevercmp/filevercmp.c +[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/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/split.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/split.cpp In file included from /usr/include/c++/10/vector:67, from /build/libvcflib-1.0.2+dfsg/src/var.hpp:17, from /build/libvcflib-1.0.2+dfsg/src/var.cpp:20: @@ -796,6 +865,8 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvcflib.so.1 -o libvcflib.so.1 CMakeFiles/vcflib.dir/src/Variant.cpp.o CMakeFiles/vcflib.dir/src/rnglib.cpp.o CMakeFiles/vcflib.dir/src/var.cpp.o CMakeFiles/vcflib.dir/src/pdflib.cpp.o CMakeFiles/vcflib.dir/src/cdflib.cpp.o CMakeFiles/vcflib.dir/src/split.cpp.o CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -lssw -ltabixpp -lsmithwaterman -ldisorder -lfastahack @@ -805,68 +876,57 @@ make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend -make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend -make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake --color= +make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglbound.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsample2info.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2dag.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfindex.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2dag.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2dag.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2dag.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfindex.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfindex.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfindex.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsample2info.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsample2info.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsample2info.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfinfosummarize.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfinfosummarize.dir/depend.internal". -Scanning dependencies of target vcfindex -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglbound.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglbound.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglbound.dir/depend.internal". -Scanning dependencies of target vcfsample2info Scanning dependencies of target vcfinfosummarize make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build -Scanning dependencies of target vcf2dag -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsample2info.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsample2info.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsample2info.dir/depend.internal". +Scanning dependencies of target vcfsample2info +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglbound.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglbound.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglbound.dir/depend.internal". Scanning dependencies of target vcfglbound -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2dag.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2dag.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2dag.dir/depend.internal". make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build +[ 5%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfinfosummarize.cpp +Scanning dependencies of target vcf2dag make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 6%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -[ 7%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -[ 7%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfindex.cpp +[ 6%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o +[ 6%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfglbound.cpp /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfsample2info.cpp -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfinfosummarize.cpp -[ 8%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o +[ 7%] 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 -[ 8%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfglbound.cpp In file included from /usr/include/c++/10/queue:62, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:23, - from /build/libvcflib-1.0.2+dfsg/src/vcfsample2info.cpp:10: + from /build/libvcflib-1.0.2+dfsg/src/vcfinfosummarize.cpp:10: /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/queue:62, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:23, - from /build/libvcflib-1.0.2+dfsg/src/vcfinfosummarize.cpp:10: + from /build/libvcflib-1.0.2+dfsg/src/vcfsample2info.cpp:10: /usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, @@ -878,13 +938,6 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfsample2info.cpp:10: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, from /build/libvcflib-1.0.2+dfsg/src/vcfglbound.cpp:10: @@ -899,28 +952,48 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, +In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, from /build/libvcflib-1.0.2+dfsg/src/vcfsample2info.cpp:10: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/vcfinfosummarize.cpp:10: /usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfinfosummarize.cpp:10: + from /build/libvcflib-1.0.2+dfsg/src/vcfsample2info.cpp:10: /usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 9%] Linking CXX executable vcfglbound +[ 8%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 10%] Linking CXX executable vcfindex -/usr/bin/cmake -E cmake_link_script 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/build/libvcflib-1.0.2+dfsg /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfindex.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfindex.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfindex.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfindex.dir/depend.internal". +Scanning dependencies of target vcfindex +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 9%] 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 +[ 10%] Linking CXX executable vcfinfosummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfosummarize.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 10%] Built target vcfinfosummarize make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake --color= @@ -930,10 +1003,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 11%] 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 -[ 11%] Built target vcfindex +[ 11%] Linking CXX executable vcfsample2info +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 11%] Built target vcfsample2info make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake --color= @@ -945,11 +1021,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 12%] 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 -[ 12%] Linking CXX executable vcfsample2info -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 12%] Linking CXX executable vcf2dag +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 12%] Built target vcfsample2info +[ 12%] Built target vcf2dag make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfevenregions.dir/DependInfo.cmake --color= @@ -961,11 +1037,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 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 -[ 14%] Linking CXX executable vcfinfosummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfosummarize.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 14%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 14%] Built target vcfinfosummarize +[ 14%] Built target vcfindex make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color= @@ -977,11 +1053,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 14%] 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 -[ 14%] Linking CXX executable vcf2dag -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 15%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 14%] Built target vcf2dag +[ 15%] Built target vcfgenosummarize make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= @@ -991,30 +1067,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 14%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o +[ 15%] 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 -In file included from /usr/include/c++/10/vector:72, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfcreatemulti.cpp:10: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfcreatemulti.cpp:10: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 15%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 15%] Built target vcfgenosummarize +[ 15%] Built target vcfevenregions make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2fasta.dir/DependInfo.cmake --color= @@ -1024,31 +1083,25 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 16%] 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 -[ 16%] Built target vcfevenregions -make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/depend.internal". -Scanning dependencies of target vcfremap -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfgeno2haplo.cpp:10: + from /build/libvcflib-1.0.2+dfsg/src/vcfcreatemulti.cpp:10: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 16%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfremap.cpp +In file included from /usr/include/c++/10/vector:67, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/vcfcreatemulti.cpp:10: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfbreakmulti.cpp:10: + from /build/libvcflib-1.0.2+dfsg/src/vcfgeno2haplo.cpp:10: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: @@ -1060,6 +1113,13 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:72, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/vcfbreakmulti.cpp:10: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, from /build/libvcflib-1.0.2+dfsg/src/vcfbreakmulti.cpp:10: @@ -1067,11 +1127,27 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 17%] Linking CXX executable vcfcreatemulti +[ 17%] Linking CXX executable vcfbreakmulti +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 17%] Built target vcfbreakmulti +make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/depend.internal". +Scanning dependencies of target vcfremap +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 18%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 18%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfremap.cpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 17%] Built target vcfcreatemulti +[ 18%] Built target vcfcreatemulti make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake --color= @@ -1081,13 +1157,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 18%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o +[ 19%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfuniqalleles.cpp -[ 19%] Linking CXX executable vcfbreakmulti -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 19%] Linking CXX executable vcf2fasta +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 19%] Built target vcfbreakmulti +[ 19%] Built target vcf2fasta make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfuniq.dir/DependInfo.cmake --color= @@ -1099,11 +1175,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 20%] 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 -[ 20%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 20%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 20%] Built target vcfuniqalleles +[ 20%] Built target vcfgeno2haplo make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcheck.dir/DependInfo.cmake --color= @@ -1115,11 +1191,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 20%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcheck.cpp -[ 20%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 20%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 20%] Built target vcfgeno2haplo +[ 20%] Built target vcfuniqalleles make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcombine.dir/DependInfo.cmake --color= @@ -1147,11 +1223,14 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 22%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfroc.cpp -[ 23%] Linking CXX executable vcfremap +[ 23%] Linking CXX executable vcfcheck +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 24%] Linking CXX executable vcfremap /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -o vcfremap -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 23%] Built target vcfremap +[ 24%] Built target vcfcheck make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake --color= @@ -1161,13 +1240,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 23%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o +[ 24%] 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 -[ 23%] Linking CXX executable vcf2fasta -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 23%] Built target vcf2fasta +[ 24%] Built target vcfremap make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfqual2info.dir/DependInfo.cmake --color= @@ -1177,24 +1253,8 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 24%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o +[ 25%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[ 25%] Linking CXX executable vcfcheck -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 25%] Built target vcfcheck -make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/depend.internal". -Scanning dependencies of target vcfstreamsort -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 25%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfstreamsort.cpp In file included from /usr/include/c++/10/map:60, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:15, from /build/libvcflib-1.0.2+dfsg/src/vcfroc.cpp:10: @@ -1207,29 +1267,24 @@ [ 25%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -In file included from /usr/include/c++/10/vector:72, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfstreamsort.cpp:10: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 25%] Built target vcfqual2info +make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/depend.internal". +Scanning dependencies of target vcfstreamsort +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 25%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfstreamsort.cpp [ 26%] Linking CXX executable vcfgenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -In file included from /usr/include/c++/10/map:61, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:15, - from /build/libvcflib-1.0.2+dfsg/src/vcfroc.cpp:10: -/usr/include/c++/10/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]': -/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 - 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 502 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 503 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 26%] Built target vcfqual2info +[ 26%] Built target vcfgenotypes make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/abba-baba.dir/DependInfo.cmake --color= @@ -1241,8 +1296,22 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 26%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/abba-baba.cpp +In file included from /usr/include/c++/10/map:61, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:15, + from /build/libvcflib-1.0.2+dfsg/src/vcfroc.cpp:10: +/usr/include/c++/10/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]': +/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 + 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 502 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 503 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +[ 26%] Linking CXX executable vcfcombine +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 26%] Built target vcfgenotypes +[ 26%] Built target vcfcombine make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/segmentFst.dir/DependInfo.cmake --color= @@ -1254,29 +1323,6 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 26%] Building CXX object CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/segmentFst.cpp -In file included from /usr/include/c++/10/vector:67, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfstreamsort.cpp:10: -/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 26%] Linking CXX executable vcfcombine -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 26%] Built target vcfcombine -make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/depend.internal". -Scanning dependencies of target vcfhethomratio -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 27%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfhethomratio.cpp In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/split.h:15, from /build/libvcflib-1.0.2+dfsg/src/segmentFst.cpp:59: @@ -1288,38 +1334,6 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 28%] Linking CXX executable vcfstreamsort -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstreamsort.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 28%] Built target vcfstreamsort -make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/meltEHH.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/meltEHH.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/meltEHH.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/meltEHH.dir/depend.internal". -Scanning dependencies of target meltEHH -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 29%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/meltEHH.cpp -[ 30%] Linking CXX executable segmentFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -o segmentFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 30%] Built target segmentFst -make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/depend.internal". -Scanning dependencies of target vcffilter -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 31%] 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/include/c++/10/bits/stl_map.h: In function 'int main(int, char**)': /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, @@ -1363,27 +1377,89 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 31%] Linking CXX executable vcfroc -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 32%] Linking CXX executable abba-baba +[ 27%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /usr/include/c++/10/vector:72, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/vcfstreamsort.cpp:10: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 27%] Built target segmentFst +make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/depend.internal". +Scanning dependencies of target vcfhethomratio +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 28%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfhethomratio.cpp +In file included from /usr/include/c++/10/vector:67, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/vcfstreamsort.cpp:10: +/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 29%] Linking CXX executable abba-baba /usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -o abba-baba -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 32%] Built target vcfroc +[ 29%] Built target abba-baba +make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/meltEHH.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/meltEHH.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/meltEHH.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/meltEHH.dir/depend.internal". +Scanning dependencies of target meltEHH +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 30%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/meltEHH.cpp +[ 30%] Linking CXX executable vcfroc +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 31%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 31%] Built target vcfstreamsort +make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/depend.internal". +[ 31%] Built target vcfroc +Scanning dependencies of target vcffilter make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfclassify.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfclassify.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfclassify.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfclassify.dir/depend.internal". Scanning dependencies of target vcfclassify make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 32%] 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 [ 33%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfclassify.cpp +[ 33%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 33%] Built target abba-baba +[ 33%] Built target vcfhethomratio make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake --color= @@ -1402,22 +1478,14 @@ /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 33%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 33%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 33%] Built target vcfhethomratio +[ 33%] Built target vcfclassify make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosamplenames.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosamplenames.dir/depend.internal". -Scanning dependencies of target vcfgenosamplenames -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 34%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgenosamplenames.cpp In file included from /usr/include/c++/10/map:61, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:15, from /build/libvcflib-1.0.2+dfsg/src/meltEHH.cpp:10: @@ -1436,6 +1504,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosamplenames.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosamplenames.dir/depend.internal". +Scanning dependencies of target vcfgenosamplenames +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 34%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgenosamplenames.cpp /usr/include/c++/10/bits/stl_map.h: In function 'void loadGeneticMap(int, int)': /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, @@ -1444,8 +1520,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 34%] Linking CXX executable vcfclassify -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, from /build/libvcflib-1.0.2+dfsg/src/meltEHH.cpp:10: @@ -1453,9 +1527,11 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 35%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 34%] Built target vcfclassify +[ 35%] Built target vcfaddinfo make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfaltcount.dir/DependInfo.cmake --color= @@ -1465,13 +1541,20 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 35%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o +[ 36%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfaltcount.cpp -[ 36%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /usr/include/c++/10/vector:67, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/meltEHH.cpp:10: +/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 36%] Built target vcffilter +[ 37%] Built target meltEHH make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhetcount.dir/DependInfo.cmake --color= @@ -1481,23 +1564,16 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 37%] Building CXX object CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o +[ 38%] 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 -In file included from /usr/include/c++/10/vector:67, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/meltEHH.cpp:10: -/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 38%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 38%] Linking CXX executable vcfgenosamplenames /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 39%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 38%] Built target vcfaddinfo +[ 39%] Built target vcfgenosamplenames make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pFst.dir/DependInfo.cmake --color= @@ -1507,10 +1583,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 38%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o +[ 39%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/pFst.dir/src/pFst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/pFst.cpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 38%] Built target vcfgenosamplenames +[ 39%] Built target vcffilter make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/plotHaps.dir/DependInfo.cmake --color= @@ -1520,14 +1596,11 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 39%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o +[ 40%] 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 -[ 39%] Linking CXX executable vcfaltcount +[ 40%] Linking CXX executable vcfaltcount /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 40%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' [ 40%] Built target vcfaltcount make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend @@ -1541,8 +1614,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 40%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o 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'/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfld.dir/DependInfo.cmake --color= @@ -1554,11 +1630,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 41%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/smoother.dir/DependInfo.cmake --color= @@ -1568,7 +1644,7 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 42%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o +[ 43%] 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 In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, @@ -1584,73 +1660,73 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:72, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfld.cpp:10: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfld.cpp:10: -/usr/include/c++/10/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 43%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 44%] Linking CXX executable pFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 44%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 43%] Built target vcfinfo2qual +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 44%] Built target pFst make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend +[ 44%] Built target plotHaps +make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfprimers.dir/DependInfo.cmake --color= Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremovesamples.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremovesamples.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfprimers.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfprimers.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfprimers.dir/depend.internal". Scanning dependencies of target vcfremovesamples make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 43%] Building CXX object CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o +Scanning dependencies of target vcfprimers +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 44%] 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 -[ 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 43%] Linking CXX executable smoother +[ 45%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfprimers.cpp +[ 45%] Linking CXX executable smoother /usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 43%] Built target plotHaps -make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf 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Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandom.dir/depend.internal". Scanning dependencies of target vcfrandom make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 44%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfprimers.cpp -[ 45%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o +[ 46%] 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 -[ 46%] Linking CXX executable vcfld -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /usr/include/c++/10/vector:72, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/vcfld.cpp:10: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/vcfld.cpp:10: +/usr/include/c++/10/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 46%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 46%] Built target vcfld +[ 46%] Built target vcfprimers make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/iHS.dir/DependInfo.cmake --color= @@ -1662,11 +1738,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 47%] Building CXX object CMakeFiles/iHS.dir/src/iHS.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/iHS.dir/src/iHS.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/iHS.cpp -[ 48%] Linking CXX executable pFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 48%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 48%] Built target pFst +[ 48%] Built target vcfremovesamples make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake --color= @@ -1678,14 +1754,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 49%] 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 -[ 50%] Linking CXX executable vcfremovesamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -o vcfremovesamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 50%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 50%] Linking CXX executable vcfld +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 50%] Built target vcfremovesamples +[ 50%] Built target vcfld make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfafpath.dir/DependInfo.cmake --color= @@ -1697,37 +1770,9 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 50%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfafpath.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 50%] Built target vcfprimers -make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfecho.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfecho.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfecho.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfecho.dir/depend.internal". -Scanning dependencies of target vcfecho -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 51%] Building CXX object CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfecho.cpp -[ 51%] Linking CXX executable vcfrandom +[ 50%] Linking CXX executable vcfrandom /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 51%] Built target vcfrandom -make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/depend.internal". -Scanning dependencies of target genotypeSummary -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 52%] Building CXX object CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/genotypeSummary.cpp -[ 52%] Linking CXX executable vcfecho -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1 In file included from /usr/include/c++/10/map:60, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:15, from /build/libvcflib-1.0.2+dfsg/src/iHS.cpp:10: @@ -1735,50 +1780,19 @@ /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 52%] Built target vcfecho -make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsitesummarize.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsitesummarize.dir/depend.internal". -Scanning dependencies of target vcfsitesummarize -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 52%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfsitesummarize.cpp -[ 52%] Linking CXX executable vcfkeepgeno -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1 -In file included from /usr/include/c++/10/vector:72, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfafpath.cpp:10: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 52%] Built target vcfkeepgeno -make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend +[ 50%] Built target vcfrandom +make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/depend.internal". -Scanning dependencies of target vcfcommonsamples +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfecho.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfecho.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfecho.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfecho.dir/depend.internal". +Scanning dependencies of target vcfecho make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build +make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 53%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcommonsamples.cpp -In file included from /usr/include/c++/10/vector:67, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfafpath.cpp:10: -/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 51%] Building CXX object CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfecho.cpp In file included from /usr/include/c++/10/map:61, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:15, from /build/libvcflib-1.0.2+dfsg/src/iHS.cpp:10: @@ -1807,16 +1821,85 @@ | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/vcfafpath.cpp:10: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 51%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /usr/include/c++/10/vector:72, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, from /build/libvcflib-1.0.2+dfsg/src/iHS.cpp:10: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 54%] Linking CXX executable vcfafpath +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 51%] Built target vcfkeepgeno +make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/depend.internal". +Scanning dependencies of target genotypeSummary +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +In file included from /usr/include/c++/10/vector:67, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/vcfafpath.cpp:10: +/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 52%] Building CXX object CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/genotypeSummary.cpp +In file included from /usr/include/c++/10/vector:67, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/iHS.cpp:10: +/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 52%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 53%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 54%] Built target vcfafpath +[ 53%] Built target vcfecho +make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsitesummarize.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsitesummarize.dir/depend.internal". +Scanning dependencies of target vcfsitesummarize +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 53%] 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 +[ 53%] Built target vcfafpath +make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/depend.internal". +Scanning dependencies of target vcfcommonsamples +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 54%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcommonsamples.cpp +[ 54%] Linking CXX executable iHS +/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 54%] Built target iHS make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/bFst.dir/DependInfo.cmake --color= @@ -1828,11 +1911,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 54%] Building CXX object CMakeFiles/bFst.dir/src/bFst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/bFst.dir/src/bFst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/bFst.cpp -[ 55%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 55%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 55%] Built target vcfsitesummarize +[ 55%] Built target vcfcommonsamples make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfentropy.dir/DependInfo.cmake --color= @@ -1844,18 +1927,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 56%] 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 -In file included from /usr/include/c++/10/vector:67, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/iHS.cpp:10: -/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 57%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 57%] Linking CXX executable vcfsitesummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 57%] Built target vcfcommonsamples +[ 57%] Built target vcfsitesummarize make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/permuteSmooth.dir/DependInfo.cmake --color= @@ -1865,54 +1941,11 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 57%] Linking CXX executable genotypeSummary -/usr/bin/cmake -E cmake_link_script CMakeFiles/genotypeSummary.dir/link.txt --verbose=1 [ 58%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/permuteSmooth.cpp +[ 58%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 58%] Built target genotypeSummary -make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremoveaberrantgenotypes.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremoveaberrantgenotypes.dir/depend.internal". -Scanning dependencies of target vcfremoveaberrantgenotypes -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 58%] 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 -[ 58%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 58%] Built target iHS -make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pVst.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pVst.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pVst.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pVst.dir/depend.internal". -Scanning dependencies of target pVst -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 58%] Building CXX object CMakeFiles/pVst.dir/src/pVst.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/pVst.dir/src/pVst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/pVst.cpp -In file included from /usr/include/c++/10/vector:72, - from /build/libvcflib-1.0.2+dfsg/src/split.h:15, - from /build/libvcflib-1.0.2+dfsg/src/permuteSmooth.cpp:49: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from /build/libvcflib-1.0.2+dfsg/src/split.h:15, - from /build/libvcflib-1.0.2+dfsg/src/permuteSmooth.cpp:49: -/usr/include/c++/10/bits/stl_vector.h: In function 'bool getContiguousWindow(std::vector&, std::vector&, int, int*)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, from /build/libvcflib-1.0.2+dfsg/src/bFst.cpp:10: @@ -1937,6 +1970,19 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 58%] Built target genotypeSummary +make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremoveaberrantgenotypes.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremoveaberrantgenotypes.dir/depend.internal". +Scanning dependencies of target vcfremoveaberrantgenotypes +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 58%] 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 In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, from /build/libvcflib-1.0.2+dfsg/src/bFst.cpp:10: @@ -1954,21 +2000,51 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 59%] Linking CXX executable vcfremoveaberrantgenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /usr/include/c++/10/vector:72, + from /build/libvcflib-1.0.2+dfsg/src/split.h:15, + from /build/libvcflib-1.0.2+dfsg/src/permuteSmooth.cpp:49: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/10/vector:67, + from /build/libvcflib-1.0.2+dfsg/src/split.h:15, + from /build/libvcflib-1.0.2+dfsg/src/permuteSmooth.cpp:49: +/usr/include/c++/10/bits/stl_vector.h: In function 'bool getContiguousWindow(std::vector&, std::vector&, int, int*)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function 'int main(int, char**)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 59%] Linking CXX executable permuteSmooth +[ 58%] Linking CXX executable permuteSmooth /usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 -[ 59%] Built target vcfremoveaberrantgenotypes +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 58%] Built target permuteSmooth +make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pVst.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pVst.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pVst.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pVst.dir/depend.internal". +Scanning dependencies of target pVst +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 58%] Building CXX object CMakeFiles/pVst.dir/src/pVst.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/pVst.dir/src/pVst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/pVst.cpp +[ 59%] Linking CXX executable bFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 59%] Linking CXX executable vcfentropy +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 59%] Built target bFst make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/permuteGPAT++.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/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/permuteGPAT++.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/permuteGPAT++.dir/depend.internal". Scanning dependencies of target permuteGPAT++ @@ -1978,7 +2054,7 @@ [ 60%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/permuteGPAT++.cpp make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 60%] Built target permuteSmooth +[ 60%] Built target vcfentropy make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake --color= @@ -1990,22 +2066,9 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 60%] 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 -[ 60%] Linking CXX executable vcfentropy -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 60%] Built target vcfentropy -make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/depend.internal". -Scanning dependencies of target vcfgenotypecompare -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 60%] 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 +[ 61%] Linking CXX executable vcfremoveaberrantgenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/split.h:15, from /build/libvcflib-1.0.2+dfsg/src/permuteGPAT++.cpp:49: @@ -2020,9 +2083,51 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 61%] Linking CXX executable bFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 61%] Built target vcfremoveaberrantgenotypes +make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/depend.internal". +Scanning dependencies of target vcfgenotypecompare +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 61%] 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 +[ 61%] Linking CXX executable permuteGPAT++ +/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 61%] Built target permuteGPAT++ +make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfflatten.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfflatten.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfflatten.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfflatten.dir/depend.internal". +Scanning dependencies of target vcfflatten +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 61%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfflatten.cpp +[ 62%] Linking CXX executable dumpContigsFromHeader +/usr/bin/cmake -E cmake_link_script CMakeFiles/dumpContigsFromHeader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -o dumpContigsFromHeader -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 62%] Built target dumpContigsFromHeader +make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotate.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotate.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotate.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotate.dir/depend.internal". +Scanning dependencies of target vcfannotate +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 63%] 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 In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, from /build/libvcflib-1.0.2+dfsg/src/pVst.cpp:10: @@ -2047,23 +2152,6 @@ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 61%] Linking CXX executable permuteGPAT++ -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 -[ 61%] Built target bFst -make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfflatten.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/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf/CMakeFiles/vcfflatten.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfflatten.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfflatten.dir/depend.internal". -Scanning dependencies of target vcfflatten -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 61%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfflatten.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' /usr/include/c++/10/bits/vector.tcc: In function 'void loadDat(copyNcounts*, std::string&, std::vector, std::vector > > >&, std::vector, std::vector > > >&)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -2077,23 +2165,11 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 61%] Built target permuteGPAT++ -make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotate.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotate.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotate.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotate.dir/depend.internal". -Scanning dependencies of target vcfannotate -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 62%] 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 -[ 63%] Linking CXX executable dumpContigsFromHeader -/usr/bin/cmake -E cmake_link_script CMakeFiles/dumpContigsFromHeader.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -o dumpContigsFromHeader -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 64%] Linking CXX executable pVst +/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 63%] Built target dumpContigsFromHeader +[ 64%] Built target pVst make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/hapLrt.dir/DependInfo.cmake --color= @@ -2103,13 +2179,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 64%] Building CXX object CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o +[ 65%] 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 -[ 65%] Linking CXX executable pVst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 66%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 65%] Built target pVst +[ 66%] Built target vcfflatten make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake --color= @@ -2119,13 +2195,23 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 66%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o +[ 67%] 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 -[ 66%] Linking CXX executable vcfkeepsamples +[ 67%] Linking CXX executable vcfkeepsamples /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 68%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /usr/include/c++/10/vector:72, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/hapLrt.cpp:10: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 66%] Built target vcfkeepsamples +[ 68%] Built target vcfkeepsamples make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/normalize-iHS.dir/DependInfo.cmake --color= @@ -2135,13 +2221,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 66%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/normalize-iHS.cpp -[ 67%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 67%] Built target vcfflatten +[ 68%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/normalize-iHS.cpp +[ 68%] Built target vcfgenotypecompare make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2tsv.dir/DependInfo.cmake --color= @@ -2151,15 +2234,31 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 68%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o +[ 69%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcf2tsv.cpp -In file included from /usr/include/c++/10/vector:72, +[ 69%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 69%] Built target vcfannotate +make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/depend.internal". +Scanning dependencies of target popStats +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 70%] Building CXX object CMakeFiles/popStats.dir/src/popStats.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/popStats.dir/src/popStats.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/popStats.cpp +In file included from /usr/include/c++/10/vector:67, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, from /build/libvcflib-1.0.2+dfsg/src/hapLrt.cpp:10: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': +/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1198 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/split.h:15, from /build/libvcflib-1.0.2+dfsg/src/normalize-iHS.cpp:59: @@ -2174,37 +2273,14 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/10/vector:67, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/hapLrt.cpp:10: -/usr/include/c++/10/bits/stl_vector.h: In function 'int main(int, char**)': -/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1198 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 69%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 70%] Linking CXX executable normalize-iHS +[ 71%] Linking CXX executable normalize-iHS /usr/bin/cmake -E cmake_link_script CMakeFiles/normalize-iHS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -o normalize-iHS -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 70%] Built target normalize-iHS -make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/depend.internal". -Scanning dependencies of target popStats -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 70%] Built target vcfgenotypecompare +[ 71%] Built target normalize-iHS make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcat.dir/DependInfo.cmake --color= -[ 71%] 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 Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcat.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcat.dir/depend.internal". Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcat.dir/depend.internal". Scanning dependencies of target vcfcat @@ -2216,10 +2292,7 @@ [ 71%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 71%] Linking CXX executable vcfannotate -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 71%] Built target hapLrt make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' @@ -2232,8 +2305,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 71%] Building CXX object CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/sequenceDiversity.cpp +[ 72%] Linking CXX executable vcf2tsv +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 71%] Built target vcfannotate +[ 72%] Built target vcf2tsv make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake --color= @@ -2243,13 +2319,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 72%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o +[ 73%] 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 -[ 73%] Linking CXX executable vcf2tsv -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 74%] Linking CXX executable vcfcat +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 73%] Built target vcf2tsv +[ 74%] Built target vcfcat make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffixup.dir/DependInfo.cmake --color= @@ -2259,16 +2335,16 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 73%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o +[ 74%] 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 -[ 74%] Linking CXX executable vcfcat -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 75%] Linking CXX executable vcfsamplenames +[ 75%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 76%] Linking CXX executable vcfsamplenames /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 75%] Built target vcfcat +[ 76%] Built target popStats make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake --color= @@ -2278,10 +2354,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 76%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 76%] Built target vcfsamplenames +[ 77%] 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 +[ 77%] Built target vcfsamplenames make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color= @@ -2291,7 +2367,7 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 76%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o +[ 77%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfparsealts.cpp In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, @@ -2307,12 +2383,9 @@ /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 77%] Linking CXX executable vcfparsealts +[ 78%] Linking CXX executable vcfparsealts /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -o vcfparsealts -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 78%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' [ 78%] Built target vcfparsealts make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend @@ -2326,8 +2399,14 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 78%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfstats.cpp +[ 79%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 80%] Linking CXX executable sequenceDiversity +/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 78%] Built target popStats +[ 80%] Built target vcffixup make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfnumalt.dir/DependInfo.cmake --color= @@ -2337,13 +2416,10 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 78%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfnumalt.cpp -[ 79%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 79%] Built target vcffixup +[ 80%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfnumalt.cpp +[ 80%] Built target sequenceDiversity make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/wcFst.dir/DependInfo.cmake --color= @@ -2353,14 +2429,11 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 80%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o +[ 81%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/wcFst.dir/src/wcFst.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/wcFst.cpp -[ 80%] Linking CXX executable vcfsamplediff +[ 81%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 81%] Linking CXX executable sequenceDiversity -/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' [ 81%] Built target vcfsamplediff make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend @@ -2374,8 +2447,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 82%] 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 +[ 83%] Linking CXX executable vcfnumalt +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 82%] Built target sequenceDiversity +[ 83%] Built target vcfnumalt make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfleftalign.dir/DependInfo.cmake --color= @@ -2385,13 +2461,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 82%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o +[ 83%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfleftalign.cpp -[ 83%] Linking CXX executable vcfnumalt -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 83%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 83%] Built target vcfnumalt +[ 83%] Built target vcfcleancomplex make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglxgt.dir/DependInfo.cmake --color= @@ -2403,22 +2479,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 84%] 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 -In file included from /usr/include/c++/10/vector:72, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, - from /build/libvcflib-1.0.2+dfsg/src/vcfleftalign.cpp:10: -/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 426 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/vector.tcc: In function 'double entropy(const string&)': -/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 84%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 85%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 84%] Built target vcfcleancomplex +[ 85%] Built target wcFst make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfintersect.dir/DependInfo.cmake --color= @@ -2428,13 +2493,24 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 84%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o +[ 85%] 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 -[ 85%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /usr/include/c++/10/vector:72, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, + from /build/libvcflib-1.0.2+dfsg/src/vcfleftalign.cpp:10: +/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 426 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/vector.tcc: In function 'double entropy(const string&)': +/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 86%] Linking CXX executable vcfstats +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -o vcfstats -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 85%] Built target wcFst +[ 86%] Built target vcfstats make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake --color= @@ -2444,13 +2520,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 86%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o +[ 87%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfallelicprimitives.cpp -[ 86%] Linking CXX executable vcfglxgt +[ 87%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 86%] Built target vcfglxgt +[ 87%] Built target vcfglxgt make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake --color= @@ -2460,13 +2536,13 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 87%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o +[ 88%] 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 -[ 88%] Linking CXX executable vcfstats -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -o vcfstats -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 89%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 88%] Built target vcfstats +[ 89%] Built target vcfleftalign make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfoverlay.dir/DependInfo.cmake --color= @@ -2476,24 +2552,8 @@ make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 88%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o +[ 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 -[ 89%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 89%] Built target vcfleftalign -make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/depend.internal". -Scanning dependencies of target vcfkeepinfo -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 90%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfkeepinfo.cpp In file included from /usr/include/c++/10/map:60, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:15, from /build/libvcflib-1.0.2+dfsg/src/vcfallelicprimitives.cpp:10: @@ -2501,22 +2561,6 @@ /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 90%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 90%] Built target vcfkeepinfo -make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/depend.internal". -Scanning dependencies of target vcfgeno2alleles -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 91%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgeno2alleles.cpp In file included from /usr/include/c++/10/map:61, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:15, from /build/libvcflib-1.0.2+dfsg/src/vcfallelicprimitives.cpp:10: @@ -2528,22 +2572,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 92%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 92%] Built target vcfoverlay -make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcountalleles.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcountalleles.dir/depend.internal". -Scanning dependencies of target vcfcountalleles -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 92%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcountalleles.cpp In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, from /build/libvcflib-1.0.2+dfsg/src/vcfannotategenotypes.cpp:10: @@ -2569,17 +2597,17 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 92%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 92%] Built target vcfgeno2alleles -make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfdistance.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfdistance.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfdistance.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfdistance.dir/depend.internal". -Scanning dependencies of target vcfdistance +In file included from /usr/include/c++/10/map:60, + from /build/libvcflib-1.0.2+dfsg/src/Variant.h:15, + from /build/libvcflib-1.0.2+dfsg/src/vcfannotategenotypes.cpp:10: +/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >, std::__cxx11::basic_string, std::allocator > >&&>, std::tuple<>}; _Key = std::pair, std::__cxx11::basic_string >; _Val = std::pair, std::__cxx11::basic_string >, vcflib::Variant>; _KeyOfValue = std::_Select1st, std::__cxx11::basic_string >, vcflib::Variant> >; _Compare = std::less, std::__cxx11::basic_string > >; _Alloc = std::allocator, std::__cxx11::basic_string >, vcflib::Variant> >]': +/usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::__cxx11::basic_string >, std::pair, std::__cxx11::basic_string >, vcflib::Variant>, std::_Select1st, std::__cxx11::basic_string >, vcflib::Variant> >, std::less, std::__cxx11::basic_string > >, std::allocator, std::__cxx11::basic_string >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::__cxx11::basic_string >, std::pair, std::__cxx11::basic_string >, vcflib::Variant>, std::_Select1st, std::__cxx11::basic_string >, vcflib::Variant> >, std::less, std::__cxx11::basic_string > >, std::allocator, std::__cxx11::basic_string >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1 +[ 90%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp /usr/include/c++/10/bits/stl_map.h: In function 'int main(int, char**)': /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, @@ -2588,8 +2616,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2597,31 +2623,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 92%] 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 -In file included from /usr/include/c++/10/map:60, - from /build/libvcflib-1.0.2+dfsg/src/Variant.h:15, - from /build/libvcflib-1.0.2+dfsg/src/vcfannotategenotypes.cpp:10: -/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >, std::__cxx11::basic_string, std::allocator > >&&>, std::tuple<>}; _Key = std::pair, std::__cxx11::basic_string >; _Val = std::pair, std::__cxx11::basic_string >, vcflib::Variant>; _KeyOfValue = std::_Select1st, std::__cxx11::basic_string >, vcflib::Variant> >; _Compare = std::less, std::__cxx11::basic_string > >; _Alloc = std::allocator, std::__cxx11::basic_string >, vcflib::Variant> >]': -/usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::__cxx11::basic_string >, std::pair, std::__cxx11::basic_string >, vcflib::Variant>, std::_Select1st, std::__cxx11::basic_string >, vcflib::Variant> >, std::less, std::__cxx11::basic_string > >, std::allocator, std::__cxx11::basic_string >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::__cxx11::basic_string >, std::pair, std::__cxx11::basic_string >, vcflib::Variant>, std::_Select1st, std::__cxx11::basic_string >, vcflib::Variant> >, std::less, std::__cxx11::basic_string > >, std::allocator, std::__cxx11::basic_string >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1 -[ 93%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 93%] Built target vcfcountalleles -make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend +[ 90%] Built target vcfoverlay +make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflength.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflength.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflength.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflength.dir/depend.internal". -Scanning dependencies of target vcflength +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/depend.internal". +Scanning dependencies of target vcfkeepinfo make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build +make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 91%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfkeepinfo.cpp In file included from /usr/include/c++/10/vector:67, from /build/libvcflib-1.0.2+dfsg/src/Variant.h:13, from /build/libvcflib-1.0.2+dfsg/src/vcfannotategenotypes.cpp:10: @@ -2656,13 +2670,75 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 93%] 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 vcfintersect +[ 92%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 94%] Built target vcfintersect +[ 92%] Built target vcfintersect +make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/depend.internal". +Scanning dependencies of target vcfgeno2alleles +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 93%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfgeno2alleles.cpp +[ 94%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 94%] Built target vcfannotategenotypes +make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcountalleles.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcountalleles.dir/depend.internal". +Scanning dependencies of target vcfcountalleles +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 94%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/vcfcountalleles.cpp +[ 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 94%] Built target vcfkeepinfo +make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfdistance.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfdistance.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfdistance.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfdistance.dir/depend.internal". +Scanning dependencies of target vcfdistance +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 94%] Linking CXX executable vcfallelicprimitives +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 +[ 94%] 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 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 94%] Built target vcfallelicprimitives +make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflength.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflength.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflength.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflength.dir/depend.internal". +Scanning dependencies of target vcflength +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 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 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 94%] Built target vcfgeno2alleles make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/segmentIhs.dir/DependInfo.cmake --color= @@ -2674,6 +2750,22 @@ make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' [ 94%] Building CXX object CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.2\" -DVERSION=\"1.0.2\" -I/build/libvcflib-1.0.2+dfsg/include -I/build/libvcflib-1.0.2+dfsg/intervaltree -I/build/libvcflib-1.0.2+dfsg/multichoose -I/build/libvcflib-1.0.2+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -o CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -c /build/libvcflib-1.0.2+dfsg/src/segmentIhs.cpp +[ 95%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' +[ 95%] Built target vcfcountalleles +make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake --color= +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/depend.internal". +Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/depend.internal". +Scanning dependencies of target vcfrandomsample +make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' +[ 96%] 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 In file included from /usr/include/c++/10/vector:72, from /build/libvcflib-1.0.2+dfsg/src/split.h:15, from /build/libvcflib-1.0.2+dfsg/src/segmentIhs.cpp:59: @@ -2685,37 +2777,16 @@ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 95%] Linking CXX executable segmentIhs +[ 97%] Linking CXX executable segmentIhs /usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/libvcflib-1.0.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -o segmentIhs -Wl,-rpath,/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 96%] Linking CXX executable vcfdistance +[ 98%] 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-arm-linux-gnueabihf: 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-arm-linux-gnueabihf' -[ 96%] Built target segmentIhs -make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake --color= -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/depend.internal". -Dependee "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/depend.internal". -Scanning dependencies of target vcfrandomsample -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 97%] 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 -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 97%] Built target vcfdistance -[ 97%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 98%] 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 98%] Built target segmentIhs make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -make[4]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' -[ 98%] Built target vcfallelicprimitives -[ 98%] Built target vcfannotategenotypes +[ 98%] Built target vcfdistance [ 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-arm-linux-gnueabihf: libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lpthread -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp @@ -2741,22 +2812,22 @@ [----------] Global test environment set-up. [----------] 1 test from Variant [ RUN ] Variant.correctGenotype -[ OK ] Variant.correctGenotype (17057 ms) -[----------] 1 test from Variant (17057 ms total) +[ OK ] Variant.correctGenotype (27447 ms) +[----------] 1 test from Variant (27456 ms total) [----------] 4 tests from VariantCallFile [ RUN ] VariantCallFile.open -[ OK ] VariantCallFile.open (3 ms) +[ OK ] VariantCallFile.open (8 ms) [ RUN ] VariantCallFile.recordCountUncompressed -[ OK ] VariantCallFile.recordCountUncompressed (4 ms) +[ OK ] VariantCallFile.recordCountUncompressed (1 ms) [ RUN ] VariantCallFile.recordCountCompressed -[ OK ] VariantCallFile.recordCountCompressed (54 ms) +[ OK ] VariantCallFile.recordCountCompressed (46 ms) [ RUN ] VariantCallFile.sampleNamesCompressed -[ OK ] VariantCallFile.sampleNamesCompressed (23 ms) -[----------] 4 tests from VariantCallFile (84 ms total) +[ OK ] VariantCallFile.sampleNamesCompressed (25 ms) +[----------] 4 tests from VariantCallFile (80 ms total) [----------] Global test environment tear-down -[==========] 5 tests from 2 test suites ran. (17141 ms total) +[==========] 5 tests from 2 test suites ran. (27545 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' @@ -2764,7 +2835,7 @@ dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake - cd obj-arm-linux-gnueabihf && make -j5 install DESTDIR=/build/libvcflib-1.0.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/libvcflib-1.0.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libvcflib-1.0.2+dfsg -B/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2962,90 +3033,90 @@ -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/include/vec128int.h -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/include/veclib_types.h -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfclassify.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfkeepinfo.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenosummarize.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/wcFst.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfbreakmulti.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgeno2haplo.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsamplenames.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2dag.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfoverlay.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfparsealts.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/pFst.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/normalize-iHS.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfstats.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfflatten.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/segmentFst.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfaddinfo.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfhetcount.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfleftalign.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2tsv.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfinfo2qual.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfecho.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenosamplenames.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/permuteSmooth.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfqual2info.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfintersect.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfaltcount.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsamplediff.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2fasta.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgeno2alleles.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/smoother.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsample2info.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcountalleles.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfstreamsort.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcat.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/pVst.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/sequenceDiversity.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/popStats.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfkeepsamples.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/segmentIhs.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/meltEHH.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfinfo2qual.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfafpath.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfstats.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfevenregions.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcffilter.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/segmentFst.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfparsealts.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfprimers.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/genotypeSummary.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfkeepsamples.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/hapLrt.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfinfosummarize.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcheck.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfoverlay.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcreatemulti.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfuniq.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcffixup.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcombine.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfglbound.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfglxgt.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/pFst.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsamplediff.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfbreakmulti.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfannotate.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/dumpContigsFromHeader.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfhethomratio.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/iHS.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcommonsamples.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcat.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfremoveaberrantgenotypes.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcflength.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfuniqalleles.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfrandom.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsitesummarize.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfnumalt.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/plotHaps.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfindex.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfannotategenotypes.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcountalleles.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenotypes.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfintersect.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenotypecompare.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2tsv.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsamplenames.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/normalize-iHS.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcheck.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/sequenceDiversity.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcombine.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcflib.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfuniq.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfstreamsort.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfafpath.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/smoother.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfdistance.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfinfosummarize.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfindex.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfclassify.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfkeepinfo.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/permuteGPAT++.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfuniqalleles.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenotypecompare.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsample2info.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/pVst.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfprimers.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfallelicprimitives.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfqual2info.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfremovesamples.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/genotypeSummary.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/abba-baba.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfflatten.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfannotate.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcflib.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfremap.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenosummarize.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/hapLrt.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/wcFst.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfentropy.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfld.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfroc.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfrandomsample.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/dumpContigsFromHeader.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfnumalt.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcommonsamples.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/bFst.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcffixup.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/plotHaps.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfremap.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfglxgt.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfglbound.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/meltEHH.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcffilter.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/iHS.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfkeepgeno.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfannotategenotypes.1 -- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfcleancomplex.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfleftalign.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfremovesamples.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfentropy.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/bFst.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfroc.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfallelicprimitives.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2dag.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfaltcount.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcflength.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfhetcount.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfld.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfdistance.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfremoveaberrantgenotypes.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfecho.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfaddinfo.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgenosamplenames.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfgeno2haplo.1 --- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcf2fasta.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/popStats.1 +-- Installing: /build/libvcflib-1.0.2+dfsg/debian/tmp/usr/man/man1/man/vcfsitesummarize.1 make[1]: Leaving directory '/build/libvcflib-1.0.2+dfsg/obj-arm-linux-gnueabihf' debian/rules override_dh_install make[1]: Entering directory '/build/libvcflib-1.0.2+dfsg' @@ -3084,104 +3155,104 @@ dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libvcflib1/usr/lib/arm-linux-gnueabihf/libvcflib.so.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libvcflib1/usr/lib/arm-linux-gnueabihf/libvcflib.so.1 was not linked against libdisorder.so.0 (it uses none of the library's symbols) -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcommonsamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcfallelicprimitives contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremoveaberrantgenotypes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfallelicprimitives contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfecho contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfstats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcombine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcf2tsv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfglxgt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfnumalt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcfuniqalleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfld contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfclassify contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfannotate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremovesamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/bFst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenosummarize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenosamplenames contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfindex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremoveaberrantgenotypes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfstreamsort contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfuniqalleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfrandom contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfroc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfbreakmulti contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcffixup contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/pFst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcommonsamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfqual2info contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsitesummarize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenotypes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepsamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/normalize-iHS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcheck contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/iHS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsample2info contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcountalleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcfallelicprimitives contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfflatten contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsamplediff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgeno2alleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/wcFst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/pVst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcreatemulti contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsamplenames contains 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__aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/hapLrt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfoverlay contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfleftalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsamplenames contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfprimers contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfuniq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcflength contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcreatemulti contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/sequenceDiversity contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepsamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfannotategenotypes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremovesamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfdistance contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfstreamsort contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgeno2alleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfuniqalleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/popStats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepinfo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfrandomsample contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgeno2haplo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfaddinfo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcffilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepgeno contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfevenregions contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake +dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.2+dfsg-2_armhf.deb'. +dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.2+dfsg-2_armhf.deb'. dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.2+dfsg-2_armhf.deb'. dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.2+dfsg-2_armhf.deb'. -dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.2+dfsg-2_armhf.deb'. dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.2+dfsg-2_armhf.deb'. -dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.2+dfsg-2_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libvcflib_1.0.2+dfsg-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3189,12 +3260,14 @@ 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/8964/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/8964/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/12780 and its subdirectories -I: Current time: Tue Jul 20 22:57:05 -12 2021 -I: pbuilder-time-stamp: 1626865025 +I: removing directory /srv/workspace/pbuilder/8964 and its subdirectories +I: Current time: Thu Jul 22 01:23:21 +14 2021 +I: pbuilder-time-stamp: 1626866601