Diff of the two buildlogs: -- --- b1/build.log 2023-05-31 08:01:11.475506228 +0000 +++ b2/build.log 2023-05-31 08:13:16.827677308 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 30 19:36:31 -12 2023 -I: pbuilder-time-stamp: 1685518591 +I: Current time: Wed May 31 22:02:13 +14 2023 +I: pbuilder-time-stamp: 1685520133 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./libvcflib_1.0.3+dfsg.orig.tar.xz] I: copying [./libvcflib_1.0.3+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Oct 7 02:31:55 2022 -12 +gpgv: Signature made Sat Oct 8 04:31:55 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -35,135 +35,167 @@ dpkg-source: info: applying tests I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/10593/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/6484/tmp/hooks/D01_modify_environment starting +debug: Running on virt64c. +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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 31 22:02 /bin/sh -> /bin/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/6484/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/6484/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 parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(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 parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='28a74c57626b44cd967e80a1aae07a21' - 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='10593' - PS1='# ' - PS2='> ' + INVOCATION_ID=c1af11bf592c499a83233edab006a068 + 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=6484 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/r-b-build.QwhaB0Cr/pbuilderrc_SEFn --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QwhaB0Cr/b1 --logfile b1/build.log libvcflib_1.0.3+dfsg-2.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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/r-b-build.QwhaB0Cr/pbuilderrc_PsNi --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QwhaB0Cr/b2 --logfile b2/build.log --extrapackages usrmerge libvcflib_1.0.3+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://10.0.0.15:3142/ I: uname -a - Linux ff4a 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/10593/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 31 22:02 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/6484/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -296,7 +328,7 @@ Get: 73 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB] -Fetched 32.1 MB in 4s (8749 kB/s) +Fetched 32.1 MB in 1s (45.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (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 ... 19324 files and directories currently installed.) @@ -610,8 +642,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/libvcflib-1.0.3+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_1.0.3+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/6484/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/6484/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/libvcflib-1.0.3+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_1.0.3+dfsg-2_source.changes dpkg-buildpackage: info: source package libvcflib dpkg-buildpackage: info: source version 1.0.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -698,7 +741,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' dh_auto_build - cd obj-arm-linux-gnueabihf && make -j3 "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-1.0.3+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libvcflib-1.0.3+dfsg -B/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks @@ -710,12 +753,16 @@ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o [ 2%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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 -MD -MT CMakeFiles/vcflib.dir/src/var.cpp.o -MF CMakeFiles/vcflib.dir/src/var.cpp.o.d -o CMakeFiles/vcflib.dir/src/var.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/var.cpp -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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 -MD -MT CMakeFiles/vcflib.dir/src/rnglib.cpp.o -MF CMakeFiles/vcflib.dir/src/rnglib.cpp.o.d -o CMakeFiles/vcflib.dir/src/rnglib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/rnglib.cpp +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o [ 2%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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 -MD -MT CMakeFiles/vcflib.dir/src/pdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/pdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/pdflib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pdflib.cpp /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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 -MD -MT CMakeFiles/vcflib.dir/src/Variant.cpp.o -MF CMakeFiles/vcflib.dir/src/Variant.cpp.o.d -o CMakeFiles/vcflib.dir/src/Variant.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/Variant.cpp +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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 -MD -MT CMakeFiles/vcflib.dir/src/rnglib.cpp.o -MF CMakeFiles/vcflib.dir/src/rnglib.cpp.o.d -o CMakeFiles/vcflib.dir/src/rnglib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/rnglib.cpp +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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 -MD -MT CMakeFiles/vcflib.dir/src/var.cpp.o -MF CMakeFiles/vcflib.dir/src/var.cpp.o.d -o CMakeFiles/vcflib.dir/src/var.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/var.cpp +[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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 -MD -MT CMakeFiles/vcflib.dir/src/cdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/cdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/cdflib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/cdflib.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/Variant.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -732,8 +779,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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 -MD -MT CMakeFiles/vcflib.dir/src/pdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/pdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/pdflib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pdflib.cpp In file included from /usr/include/c++/12/vector:70, from /build/libvcflib-1.0.3+dfsg/src/var.hpp:17, from /build/libvcflib-1.0.3+dfsg/src/var.cpp:20: @@ -813,6 +858,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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 -MD -MT CMakeFiles/vcflib.dir/src/split.cpp.o -MF CMakeFiles/vcflib.dir/src/split.cpp.o.d -o CMakeFiles/vcflib.dir/src/split.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/split.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void pooled::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:185:18: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -830,10 +877,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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 -MD -MT CMakeFiles/vcflib.dir/src/cdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/cdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/cdflib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/cdflib.cpp -[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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 -MD -MT CMakeFiles/vcflib.dir/src/split.cpp.o -MF CMakeFiles/vcflib.dir/src/split.cpp.o.d -o CMakeFiles/vcflib.dir/src/split.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/split.cpp [ 4%] Building C object CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o /usr/bin/cc -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -MF CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o.d -o CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -c /build/libvcflib-1.0.3+dfsg/filevercmp/filevercmp.c [ 5%] Linking CXX shared library libvcflib.so @@ -843,29 +886,37 @@ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 5%] Built target vcflib make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfecho.dir/DependInfo.cmake --color= make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfecho.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/bFst.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build +make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pVst.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 6%] Building CXX object CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -MF CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o.d -o CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfecho.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build +make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/build +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 6%] Building CXX object CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -MF CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o.d -o CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp [ 6%] Building CXX object CMakeFiles/bFst.dir/src/bFst.cpp.o +[ 6%] Building CXX object CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o +[ 6%] Building CXX object CMakeFiles/pVst.dir/src/pVst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/bFst.dir/src/bFst.cpp.o -MF CMakeFiles/bFst.dir/src/bFst.cpp.o.d -o CMakeFiles/bFst.dir/src/bFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/bFst.cpp +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -MF CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o.d -o CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfecho.cpp +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -MF CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o.d -o CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/pVst.dir/src/pVst.cpp.o -MF CMakeFiles/pVst.dir/src/pVst.cpp.o.d -o CMakeFiles/pVst.dir/src/pVst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pVst.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -882,6 +933,22 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:10: +/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 652 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfecho.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -898,7 +965,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -919,28 +986,28 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 7%] Built target dumpContigsFromHeader -make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend +make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pVst.dir/DependInfo.cmake --color= +cd 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/usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/pVst.dir/src/pVst.cpp.o -MF CMakeFiles/pVst.dir/src/pVst.cpp.o.d -o CMakeFiles/pVst.dir/src/pVst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pVst.cpp -[ 7%] Linking CXX executable vcfecho +[ 8%] Building CXX object CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -MF CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o.d -o CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp +[ 8%] Linking CXX executable vcfecho /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 7%] Built target vcfecho -make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend +[ 8%] Built target vcfecho +make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/hapLrt.dir/DependInfo.cmake --color= +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/build +make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 8%] Building CXX object CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -MF CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o.d -o CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:10: +[ 9%] Building CXX object CMakeFiles/popStats.dir/src/popStats.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/popStats.dir/src/popStats.cpp.o -MF CMakeFiles/popStats.dir/src/popStats.cpp.o.d -o CMakeFiles/popStats.dir/src/popStats.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/popStats.cpp +In file included from /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -981,7 +1048,11 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /build/libvcflib-1.0.3+dfsg/src/popStats.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -997,10 +1068,22 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void calc(copyNcounts*)' at /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:203:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void calc(copyNcounts*)' at /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:206:25: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void loadPop(std::vector, std::vector > > >&, pop&)' at /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:73:21: @@ -1019,45 +1102,10 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:583:22: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void calc(copyNcounts*)' at /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:203:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void calc(copyNcounts*)' at /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:206:25: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 9%] Linking CXX executable bFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 9%] Built target bFst -make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 10%] Building CXX object CMakeFiles/popStats.dir/src/popStats.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/popStats.dir/src/popStats.cpp.o -MF CMakeFiles/popStats.dir/src/popStats.cpp.o.d -o CMakeFiles/popStats.dir/src/popStats.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/popStats.cpp In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void loadDat(copyNcounts*, std::string&, std::vector, std::vector > > >&, std::vector, std::vector > > >&)' at /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:265:24: @@ -1082,46 +1130,43 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/popStats.cpp:10: -/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 652 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:583:22: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 10%] Linking CXX executable bFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 10%] Built target bFst +make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/wcFst.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 11%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/wcFst.dir/src/wcFst.cpp.o -MF CMakeFiles/wcFst.dir/src/wcFst.cpp.o.d -o CMakeFiles/wcFst.dir/src/wcFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/wcFst.cpp +[ 12%] Linking CXX executable pVst +/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp:609:20: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 11%] Linking CXX executable pVst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 11%] Built target pVst -make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend +[ 12%] Built target pVst +make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/wcFst.dir/DependInfo.cmake --color= +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/iHS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/build +make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 12%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/wcFst.dir/src/wcFst.cpp.o -MF CMakeFiles/wcFst.dir/src/wcFst.cpp.o.d -o CMakeFiles/wcFst.dir/src/wcFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/wcFst.cpp +[ 13%] Building CXX object CMakeFiles/iHS.dir/src/iHS.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/iHS.dir/src/iHS.cpp.o -MF CMakeFiles/iHS.dir/src/iHS.cpp.o.d -o CMakeFiles/iHS.dir/src/iHS.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/iHS.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/wcFst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1138,19 +1183,12 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 12%] Linking CXX executable hapLrt -/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 12%] Built target hapLrt -make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/iHS.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 13%] Building CXX object CMakeFiles/iHS.dir/src/iHS.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/iHS.dir/src/iHS.cpp.o -MF CMakeFiles/iHS.dir/src/iHS.cpp.o.d -o CMakeFiles/iHS.dir/src/iHS.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/iHS.cpp +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp:609:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1180,12 +1218,25 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 14%] Building CXX object CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -MF CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o.d -o CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/segmentFst.cpp +[ 14%] Linking CXX executable hapLrt +/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /usr/include/c++/12/map:60, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:15: /usr/include/c++/12/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(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 14%] Built target hapLrt +make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/segmentIhs.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 14%] Building CXX object CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -MF CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o.d -o CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/segmentIhs.cpp In file included from /usr/include/c++/12/vector:70, from /build/libvcflib-1.0.3+dfsg/src/split.h:15, from /build/libvcflib-1.0.3+dfsg/src/segmentFst.cpp:59: @@ -1199,9 +1250,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 15%] Linking CXX executable segmentFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bool gDist(int, int, double*)' at /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:106:40: @@ -1221,16 +1269,17 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +[ 15%] Linking CXX executable segmentFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 15%] Built target segmentFst -make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/depend +make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/segmentIhs.dir/DependInfo.cmake --color= +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/build +make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 15%] Building CXX object CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -MF CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o.d -o CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/segmentIhs.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void loadGeneticMap(int, int)' at /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:151:25: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -1240,23 +1289,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 16%] Linking CXX executable wcFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 16%] Built target wcFst -In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 17%] Building CXX object CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o +[ 16%] Building CXX object CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -MF CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o.d -o CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/genotypeSummary.cpp In file included from /usr/include/c++/12/vector:70, from /build/libvcflib-1.0.3+dfsg/src/split.h:15, @@ -1271,12 +1304,27 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:648:20: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 17%] Linking CXX executable segmentIhs +/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 17%] Built target segmentIhs +make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/sequenceDiversity.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 17%] Building CXX object CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -MF CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o.d -o CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/sequenceDiversity.cpp +[ 18%] Linking CXX executable wcFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/genotypeSummary.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1293,22 +1341,22 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 18%] Linking CXX executable segmentIhs -/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:648:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 18%] Built target segmentIhs -make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/depend +[ 18%] Built target wcFst +make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/sequenceDiversity.dir/DependInfo.cmake --color= +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pFst.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/build +make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 18%] Building CXX object CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -MF CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o.d -o CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/sequenceDiversity.cpp -[ 18%] Linking CXX executable iHS -/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 18%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/pFst.dir/src/pFst.cpp.o -MF CMakeFiles/pFst.dir/src/pFst.cpp.o.d -o CMakeFiles/pFst.dir/src/pFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pFst.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/sequenceDiversity.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1325,16 +1373,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 18%] Built target iHS -make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pFst.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 18%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/pFst.dir/src/pFst.cpp.o -MF CMakeFiles/pFst.dir/src/pFst.cpp.o.d -o CMakeFiles/pFst.dir/src/pFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pFst.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/pFst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1351,6 +1389,19 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 18%] Linking CXX executable iHS +/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 18%] Built target iHS +make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/smoother.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 19%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/smoother.dir/src/smoother.cpp.o -MF CMakeFiles/smoother.dir/src/smoother.cpp.o.d -o CMakeFiles/smoother.dir/src/smoother.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/smoother.cpp In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -1361,46 +1412,54 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 18%] Linking CXX executable genotypeSummary +[ 19%] Linking CXX executable smoother +/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 19%] Linking CXX executable genotypeSummary /usr/bin/cmake -E cmake_link_script CMakeFiles/genotypeSummary.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 18%] Built target genotypeSummary -make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/smoother.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 19%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/smoother.dir/src/smoother.cpp.o -MF CMakeFiles/smoother.dir/src/smoother.cpp.o.d -o CMakeFiles/smoother.dir/src/smoother.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/smoother.cpp -[ 20%] Linking CXX executable sequenceDiversity -/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw 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/build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfld.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 22%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o +[ 20%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfld.dir/src/vcfld.cpp.o -MF CMakeFiles/vcfld.dir/src/vcfld.cpp.o.d -o CMakeFiles/vcfld.dir/src/vcfld.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfld.cpp +[ 21%] Linking CXX executable pFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 22%] Built target pFst +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 21%] Built target smoother make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/plotHaps.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 23%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o +[ 22%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -MF CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o.d -o CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/plotHaps.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfld.cpp:10: +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 22%] Built target pFst +make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/abba-baba.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 22%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -MF CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o.d -o CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/abba-baba.cpp +[ 23%] Linking CXX executable sequenceDiversity +/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 23%] Built target sequenceDiversity +make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake --color= +In file included from /build/libvcflib-1.0.3+dfsg/src/plotHaps.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1416,10 +1475,12 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 23%] Linking CXX executable smoother -/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -In file included from /build/libvcflib-1.0.3+dfsg/src/plotHaps.cpp:10: +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 24%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -MF CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o.d -o CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfld.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1435,16 +1496,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 23%] Built target smoother -make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/abba-baba.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 23%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -MF CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o.d -o CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/abba-baba.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/abba-baba.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1461,92 +1512,118 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70: +In file included from /usr/include/c++/12/vector:70, + from /build/libvcflib-1.0.3+dfsg/src/split.h:15, + from /build/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp:49: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: -/usr/include/c++/12/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++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/plotHaps.cpp:375:20: + inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp:184:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 23%] Linking CXX executable plotHaps -/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 23%] Built target plotHaps -make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 24%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -MF CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o.d -o CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp -[ 25%] 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 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 24%] Linking CXX executable permuteGPAT++ +/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 25%] Built target abba-baba +[ 24%] Built target permuteGPAT++ make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/permuteSmooth.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 26%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o +[ 25%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -MF CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o.d -o CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +/usr/include/c++/12/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++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/libvcflib-1.0.3+dfsg/src/split.h:15, - from /build/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp:49: + from /build/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp:49: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp:184:20: + inlined from 'bool getContiguousWindow(std::vector&, std::vector&, int, int*)' at /build/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp:249:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 27%] Linking CXX executable vcfld -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 27%] Linking CXX executable permuteGPAT++ -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/plotHaps.cpp:375:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 25%] Linking CXX executable permuteSmooth +/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 27%] Built target vcfld +[ 25%] Built target permuteSmooth make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/normalize-iHS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 27%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o +[ 25%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -MF CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o.d -o CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/normalize-iHS.cpp +[ 26%] 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 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 27%] Built target permuteGPAT++ +[ 26%] Built target abba-baba make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/meltEHH.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 28%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o +[ 26%] Linking CXX executable plotHaps +/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 +[ 27%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -MF CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o.d -o CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 27%] Built target plotHaps +make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfaltcount.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 28%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -MF CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o.d -o CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfaltcount.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/libvcflib-1.0.3+dfsg/src/split.h:15, + from /build/libvcflib-1.0.3+dfsg/src/normalize-iHS.cpp:59: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void normalize(std::vector&, int*)' at /build/libvcflib-1.0.3+dfsg/src/normalize-iHS.cpp:229:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1563,65 +1640,49 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/libvcflib-1.0.3+dfsg/src/split.h:15, - from /build/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp:49: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'bool getContiguousWindow(std::vector&, std::vector&, int, int*)' at /build/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp:249:19: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/libvcflib-1.0.3+dfsg/src/split.h:15, - from /build/libvcflib-1.0.3+dfsg/src/normalize-iHS.cpp:59: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void normalize(std::vector&, int*)' at /build/libvcflib-1.0.3+dfsg/src/normalize-iHS.cpp:229:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 29%] Linking CXX executable normalize-iHS +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfaltcount.cpp:10: +/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 652 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 29%] Linking CXX executable vcfld +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 30%] 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 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 29%] Built target normalize-iHS -make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend -[ 29%] Linking CXX executable permuteSmooth -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfaltcount.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 30%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -MF CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o.d -o CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfaltcount.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 30%] Built target permuteSmooth +[ 30%] Built target normalize-iHS make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhetcount.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 30%] Built target vcfld +make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake --color= [ 31%] Building CXX object CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -MF CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o.d -o CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfhetcount.cpp -In file included from /usr/include/c++/12/map:60, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:15: -/usr/include/c++/12/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(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfaltcount.cpp:10: +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 32%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -MF CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o.d -o CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfhethomratio.cpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfhethomratio.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1637,6 +1698,12 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:60, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:15: +/usr/include/c++/12/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(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfhetcount.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1653,6 +1720,19 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 32%] Linking CXX executable vcfaltcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 32%] Built target vcfaltcount +make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 33%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -MF CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o.d -o CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcffilter.cpp In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bool gDist(int, int, double*)' at /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:105:40: @@ -1681,62 +1761,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:636:20: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 31%] Linking CXX executable vcfaltcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 31%] Built target vcfaltcount -make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 32%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -MF CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o.d -o CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfhethomratio.cpp -[ 32%] Linking CXX executable vcfhetcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 32%] Built target vcfhetcount -make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 33%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -MF CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o.d -o CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcffilter.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfhethomratio.cpp:10: -/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 652 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 34%] Linking CXX executable meltEHH -/usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcffilter.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1753,16 +1777,43 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _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 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 33%] Linking CXX executable vcfhetcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:636:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 34%] Built target meltEHH +[ 33%] Built target vcfhetcount make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2tsv.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 35%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o +[ 34%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -MF CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o.d -o CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcf2tsv.cpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 34%] Built target vcfhethomratio +make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 34%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -MF CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o.d -o CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgenotypes.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2tsv.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1779,19 +1830,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 35%] Linking CXX executable vcfhethomratio -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 35%] Built target vcfhethomratio -make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 35%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -MF CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o.d -o CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgenotypes.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1808,32 +1846,19 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 36%] Linking CXX executable vcf2tsv -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 35%] Linking CXX executable meltEHH +/usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 36%] Built target vcf2tsv +[ 35%] Built target meltEHH make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 37%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o +[ 36%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -MF CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o.d -o CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp -[ 38%] Linking CXX executable vcffilter -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 38%] Built target vcffilter -make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 39%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -MF CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o.d -o CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcommonsamples.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1850,19 +1875,45 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 40%] Linking CXX executable vcfgenotypes +[ 37%] Linking CXX executable vcfgenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 40%] Built target vcfgenotypes +[ 37%] Built target vcfgenotypes +make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 38%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -MF CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o.d -o CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcommonsamples.cpp +[ 39%] Linking CXX executable vcffilter +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 39%] Built target vcffilter make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake --color= +[ 40%] Linking CXX executable vcf2tsv +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 40%] Building CXX object CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -MF CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o.d -o CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfremovesamples.cpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 40%] Built target vcf2tsv +make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 41%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -MF CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o.d -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfkeepsamples.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcommonsamples.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1895,22 +1946,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 41%] Linking CXX executable vcfcommonsamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 41%] Built target vcfcommonsamples -make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 42%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -MF CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o.d -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfkeepsamples.cpp -[ 43%] Linking CXX executable vcfremovesamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepsamples.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1927,16 +1962,51 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 42%] Linking CXX executable vcfcommonsamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 43%] Built target vcfremovesamples +[ 42%] Built target vcfcommonsamples make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 44%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o +[ 43%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -MF CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o.d -o CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfsamplenames.cpp +[ 43%] Linking CXX executable vcfkeepsamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 44%] Linking CXX executable vcfremovesamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 44%] Built target vcfremovesamples +make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color= +[ 44%] Built target vcfkeepsamples +make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffixup.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 44%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -MF CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o.d -o CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgenotypecompare.cpp +[ 44%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -MF CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o.d -o CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcffixup.cpp +In file included from /usr/include/c++/12/map:60, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:15: +/usr/include/c++/12/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(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++/12/bits/stl_tree.h:2457:7: 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 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsamplenames.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1953,18 +2023,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:60, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:15: -/usr/include/c++/12/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(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++/12/bits/stl_tree.h:2457:7: 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 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 44%] Linking CXX executable vcfkeepsamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 45%] Linking CXX executable vcfsamplenames -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /usr/include/c++/12/map:61: /usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::pair, std::__cxx11::basic_string >; _Tp = vcflib::Variant; _Compare = std::less, std::__cxx11::basic_string > >; _Alloc = std::allocator, std::__cxx11::basic_string >, vcflib::Variant> >]': /usr/include/c++/12/bits/stl_map.h:530:44: 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 @@ -1974,27 +2032,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 45%] Built target vcfkeepsamples -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color= -[ 45%] Built target vcfsamplenames -make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffixup.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 45%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -MF CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o.d -o CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgenotypecompare.cpp -[ 45%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -MF CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o.d -o CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcffixup.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcffixup.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenotypecompare.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2010,7 +2048,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenotypecompare.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcffixup.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2026,11 +2064,24 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 45%] Linking CXX executable vcfsamplenames +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 45%] Built target vcfsamplenames +make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfclassify.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 46%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -MF CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o.d -o CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfclassify.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:202:28: @@ -2060,32 +2111,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 46%] Linking CXX executable vcffixup -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 47%] Linking CXX executable vcfannotategenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 47%] Built target vcffixup -make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfclassify.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 48%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -MF CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o.d -o CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfclassify.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 48%] Built target vcfannotategenotypes -make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 49%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -MF CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o.d -o CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfclassify.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2102,36 +2127,46 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp:10: -/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 652 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +[ 47%] Linking CXX executable vcffixup +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 47%] Built target vcffixup +make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 48%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -MF CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o.d -o CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp +[ 49%] Linking CXX executable vcfannotategenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 49%] Linking CXX executable vcfclassify /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 49%] Built target vcfclassify +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 49%] Built target vcfannotategenotypes make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake --color= +[ 49%] Built target vcfclassify +make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandom.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 49%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -MF CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o.d -o CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfremoveaberrantgenotypes.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremoveaberrantgenotypes.cpp:10: +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 50%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -MF CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o.d -o CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2147,33 +2182,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 50%] Linking CXX executable vcfgenotypecompare -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 50%] Linking CXX executable vcfsamplediff -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 50%] Built target vcfgenotypecompare -make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandom.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 51%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -MF CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o.d -o CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 51%] Built target vcfsamplediff -make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 51%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfparsealts.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfparsealts.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremoveaberrantgenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2209,9 +2218,22 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 51%] Linking CXX executable vcfgenotypecompare +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 52%] Linking CXX executable vcfremoveaberrantgenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 52%] Built target vcfgenotypecompare +make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 52%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfparsealts.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 52%] Built target vcfremoveaberrantgenotypes make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend @@ -2222,19 +2244,48 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 52%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -MF CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o.d -o CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfstats.cpp -[ 53%] Linking CXX executable vcfparsealts -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 52%] Linking CXX executable vcfsamplediff +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 53%] Built target vcfparsealts +[ 52%] Built target vcfsamplediff make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfflatten.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 53%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o +[ 52%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -MF CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o.d -o CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfflatten.cpp +[ 52%] Linking CXX executable vcfrandom +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfparsealts.cpp:10: +/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 652 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 52%] Built target vcfrandom +make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfprimers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 53%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -MF CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o.d -o CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfprimers.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfstats.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2267,19 +2318,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 53%] Linking CXX executable vcfrandom -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 53%] Built target vcfrandom -make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfprimers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 54%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -MF CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o.d -o CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfprimers.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfprimers.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2296,11 +2334,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 54%] Linking CXX executable vcfprimers -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 54%] Linking CXX executable vcfparsealts +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 54%] Built target vcfprimers +[ 54%] Built target vcfparsealts make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfnumalt.dir/DependInfo.cmake --color= @@ -2309,18 +2347,18 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 54%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -MF CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o.d -o CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfnumalt.cpp -[ 55%] Linking CXX executable vcfflatten -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfflatten.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 54%] Linking CXX executable vcfprimers +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 55%] Built target vcfflatten +[ 54%] Built target vcfprimers make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 56%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o +[ 55%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcleancomplex.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfnumalt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2354,31 +2392,31 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 57%] Linking CXX executable vcfstats -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 56%] Linking CXX executable vcfflatten +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfflatten.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 57%] Built target vcfstats +[ 56%] Built target vcfflatten make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfintersect.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 57%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o +[ 56%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -MF CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o.d -o CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfintersect.cpp -[ 58%] Linking CXX executable vcfnumalt +[ 57%] Linking CXX executable vcfnumalt /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 58%] Built target vcfnumalt +[ 57%] Built target vcfnumalt make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 59%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o +[ 58%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -MF CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o.d -o CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfannotate.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfintersect.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2396,20 +2434,36 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 59%] Linking CXX executable vcfcleancomplex +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfannotate.cpp:10: +/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 652 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 58%] Linking CXX executable vcfcleancomplex /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 59%] Built target vcfcleancomplex +[ 58%] Built target vcfcleancomplex make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 60%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o +[ 59%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfannotate.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2425,7 +2479,20 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp:10: +[ 60%] Linking CXX executable vcfstats +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 60%] Built target vcfstats +make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfoverlay.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 60%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -MF CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o.d -o CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfoverlay.cpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfoverlay.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2468,19 +2535,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 60%] Linking CXX executable vcfannotate -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 60%] Built target vcfannotate -make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfoverlay.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 60%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -MF CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o.d -o CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfoverlay.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = vcflib::VariantAllele; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp:207:46: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -2499,10 +2553,34 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 61%] Linking CXX executable vcfintersect -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfoverlay.cpp:10: +[ 61%] Linking CXX executable vcfoverlay +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 +[ 61%] Linking CXX executable vcfannotate +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 61%] Built target vcfoverlay +make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend +[ 61%] Built target vcfannotate +make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 61%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -MF CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o.d -o CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp +[ 62%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -MF CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o.d -o CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfkeepinfo.cpp +[ 63%] Linking CXX executable vcfintersect +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2518,17 +2596,9 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 61%] Built target vcfintersect -make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 61%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -MF CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o.d -o CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp:10: +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepinfo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2544,24 +2614,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 61%] Linking CXX executable vcfallelicprimitives -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 61%] Built target vcfallelicprimitives -make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 62%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -MF CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o.d -o CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfkeepinfo.cpp -[ 63%] Linking CXX executable vcfaddinfo -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 63%] Built target vcfaddinfo +[ 63%] Built target vcfintersect make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake --color= @@ -2570,7 +2624,20 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 64%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -MF CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o.d -o CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfkeepgeno.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepinfo.cpp:10: +[ 64%] Linking CXX executable vcfallelicprimitives +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 64%] Built target vcfallelicprimitives +make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfafpath.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 64%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -MF CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o.d -o CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepgeno.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2586,7 +2653,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepgeno.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2602,21 +2669,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 65%] Linking CXX executable vcfoverlay -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 65%] Built target vcfoverlay -make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfafpath.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 65%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -MF CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o.d -o CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp +[ 65%] Linking CXX executable vcfaddinfo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1 [ 65%] Linking CXX executable vcfkeepinfo /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 65%] Built target vcfkeepinfo @@ -2624,34 +2681,15 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 65%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -MF CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o.d -o CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcountalleles.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp:10: -/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 652 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 65%] Linking CXX executable vcfkeepgeno -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 65%] Built target vcfkeepgeno +[ 65%] Built target vcfaddinfo make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflength.dir/DependInfo.cmake --color= +[ 65%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -MF CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o.d -o CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcountalleles.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' @@ -2673,6 +2711,12 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 65%] Linking CXX executable vcfkeepgeno In file included from /build/libvcflib-1.0.3+dfsg/src/vcflength.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2689,43 +2733,30 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp:78:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 66%] Linking CXX executable vcfcountalleles -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 66%] Built target vcfcountalleles +[ 65%] Built target vcfkeepgeno make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfdistance.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 66%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o +[ 65%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -MF CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o.d -o CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfdistance.cpp -[ 67%] Linking CXX executable vcfafpath +[ 66%] Linking CXX executable vcfafpath /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1 +[ 67%] Linking CXX executable vcfcountalleles /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 67%] Built target vcfafpath -make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 68%] Building CXX object CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -MF CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o.d -o CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfrandomsample.cpp +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfdistance.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2742,18 +2773,25 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 69%] Linking CXX executable vcflength -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 69%] Built target vcflength +[ 67%] Built target vcfcountalleles +make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 68%] Building CXX object CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -MF CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o.d -o CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfrandomsample.cpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 68%] Built target vcfafpath make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfentropy.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 70%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o +[ 69%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -MF CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o.d -o CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfentropy.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfrandomsample.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2787,19 +2825,22 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 71%] Linking CXX executable vcfdistance -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 70%] Linking CXX executable vcflength +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 71%] Built target vcfdistance +[ 70%] Built target vcflength make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglxgt.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 72%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o +[ 71%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -MF CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o.d -o CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfglxgt.cpp +[ 72%] Linking CXX executable vcfdistance +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfglxgt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2816,32 +2857,16 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 72%] Linking CXX executable vcfentropy -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 73%] Linking CXX executable vcfrandomsample -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 73%] Built target vcfentropy +[ 72%] Built target vcfdistance make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfroc.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 74%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o +[ 73%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -MF CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o.d -o CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 74%] Built target vcfrandomsample -make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcheck.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 74%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -MF CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o.d -o CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcheck.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2858,6 +2883,32 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 73%] Linking CXX executable vcfentropy +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 73%] Built target vcfentropy +make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcheck.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 73%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -MF CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o.d -o CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcheck.cpp +[ 74%] Linking CXX executable vcfrandomsample +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 74%] Built target vcfrandomsample +make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 74%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -MF CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o.d -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcheck.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2879,26 +2930,13 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 74%] Built target vcfglxgt -make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 74%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -MF CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o.d -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp -[ 75%] Linking CXX executable vcfcheck -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 75%] Built target vcfcheck make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfuniq.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 76%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o +[ 75%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -MF CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o.d -o CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfuniq.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2932,6 +2970,19 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 76%] Linking CXX executable vcfcheck +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 76%] Built target vcfcheck +make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 77%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -MF CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o.d -o CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfuniqalleles.cpp In file included from /usr/include/c++/12/map:60, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:15: /usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long double; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]': @@ -2940,6 +2991,22 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long double; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfuniqalleles.cpp:10: +/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 652 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long double; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/map:61: @@ -2951,20 +3018,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 76%] Linking CXX executable vcfuniq +[ 77%] Linking CXX executable vcfuniq /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 76%] Built target vcfuniq -make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend +[ 77%] Built target vcfuniq +make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake --color= +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build +make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 77%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -MF CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o.d -o CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfuniqalleles.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfuniqalleles.cpp:10: +[ 77%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -MF CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o.d -o CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfremap.cpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremap.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2980,6 +3047,24 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 77%] Linking CXX executable vcfuniqalleles +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 77%] Built target vcfuniqalleles +make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2fasta.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 78%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -MF CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o.d -o CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcf2fasta.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:257:33: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 @@ -3043,34 +3128,13 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp:117:71: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 77%] Linking CXX executable vcfuniqalleles -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 77%] Built target vcfuniqalleles -make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 77%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -MF CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o.d -o CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfremap.cpp -[ 77%] Linking CXX executable vcfroc -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremap.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2fasta.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -3086,20 +3150,13 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 77%] Built target vcfroc -make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2fasta.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 78%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -MF CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o.d -o CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcf2fasta.cpp [ 79%] Linking CXX executable vcfstreamsort /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstreamsort.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 79%] Linking CXX executable vcfroc make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 79%] Built target vcfstreamsort make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' @@ -3109,7 +3166,17 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 79%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -MF CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o.d -o CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfsitesummarize.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2fasta.cpp:10: +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 79%] Built target vcfroc +make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 79%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -MF CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o.d -o CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsitesummarize.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -3125,7 +3192,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsitesummarize.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -3141,48 +3208,19 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 80%] Linking CXX executable vcfsitesummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 80%] Built target vcfsitesummarize -make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 80%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -MF CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o.d -o CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp -[ 81%] Linking CXX executable vcfremap +[ 80%] Linking CXX executable vcfremap /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 81%] Built target vcfremap +[ 80%] Built target vcfremap make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 81%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o +[ 80%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -MF CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o.d -o CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcreatemulti.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp:10: -/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 652 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcreatemulti.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -3199,10 +3237,13 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 81%] Linking CXX executable vcf2fasta +[ 80%] Linking CXX executable vcf2fasta /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 81%] Linking CXX executable vcfsitesummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 81%] Built target vcf2fasta make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' @@ -3217,6 +3258,22 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 82%] Built target vcfsitesummarize +make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcat.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 82%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -MF CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o.d -o CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcat.cpp +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]', + inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp:100:31: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfevenregions.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -3233,35 +3290,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]', - inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp:100:31: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 83%] Linking CXX executable vcfbreakmulti -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 83%] Built target vcfbreakmulti -make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcat.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 83%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -MF CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o.d -o CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcat.cpp -In file included from /usr/include/c++/12/vector:64: -/usr/include/c++/12/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++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcat.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -3278,11 +3306,21 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 83%] Linking CXX executable vcfevenregions -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 83%] Linking CXX executable vcfbreakmulti +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 83%] Built target vcfevenregions +In file included from /usr/include/c++/12/vector:64: +/usr/include/c++/12/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++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 83%] Built target vcfbreakmulti make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake --color= @@ -3291,8 +3329,20 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 84%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -MF CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o.d -o CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgenosummarize.cpp -[ 85%] Linking CXX executable vcfcreatemulti -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 +[ 85%] Linking CXX executable vcfcat +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 85%] Built target vcfcat +make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake --color= +[ 85%] Linking CXX executable vcfevenregions +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenosummarize.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -3309,30 +3359,21 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 85%] Built target vcfcreatemulti -make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 86%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -MF CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o.d -o CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgenosamplenames.cpp -[ 87%] Linking CXX executable vcfcat -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 87%] Built target vcfcat +[ 86%] Built target vcfevenregions make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 88%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o +[ 87%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -MF CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o.d -o CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgeno2haplo.cpp +[ 88%] Linking CXX executable vcfcreatemulti +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenosamplenames.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -3349,6 +3390,9 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 88%] Built target vcfcreatemulti +make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgeno2haplo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -3365,33 +3409,67 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 89%] Linking CXX executable vcfgenosummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 89%] Built target vcfgenosummarize -make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfleftalign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 89%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o +[ 88%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -MF CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o.d -o CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp -[ 89%] Linking CXX executable vcfgenosamplenames +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp:10: +/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 652 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 88%] Linking CXX executable vcfgenosamplenames /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 +[ 89%] Linking CXX executable vcfgenosummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 89%] Built target vcfgenosamplenames make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcombine.dir/DependInfo.cmake --color= +[ 89%] Built target vcfgenosummarize +make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build [ 90%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -MF CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o.d -o CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp:10: +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 91%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -MF CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o.d -o CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'double entropy(const std::string&)' at /build/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp:140:24: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -3407,7 +3485,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -3424,17 +3502,6 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'double entropy(const std::string&)' at /build/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp:140:24: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -3444,61 +3511,19 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 90%] Linking CXX executable vcfgeno2haplo -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 90%] Built target vcfgeno2haplo -make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 91%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -MF CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o.d -o CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp -[ 92%] Linking CXX executable vcfleftalign -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 91%] Linking CXX executable vcfgeno2alleles +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 92%] Built target vcfleftalign +[ 91%] Built target vcfgeno2alleles make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfindex.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 93%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o +[ 92%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -MF CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o.d -o CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfindex.cpp -[ 93%] Linking CXX executable vcfcombine -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 93%] Built target vcfcombine -make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf 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CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -MF CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o.d -o CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp:10: -/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 652 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfindex.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -3515,6 +3540,32 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 93%] Linking CXX executable vcfleftalign +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 93%] Built target vcfleftalign +make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2dag.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 94%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -MF CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o.d -o CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp +[ 94%] Linking CXX executable vcfgeno2haplo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 94%] Built target vcfgeno2haplo +make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf 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CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -MF CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o.d -o CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -3531,32 +3582,20 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 94%] Linking CXX executable vcfgeno2alleles -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 94%] Built target vcfgeno2alleles -make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsample2info.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 95%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -MF CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o.d -o CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp +[ 95%] Linking CXX executable vcfcombine +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 96%] Linking CXX executable vcfindex /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 96%] Built target vcfindex +[ 96%] Built target vcfcombine make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfqual2info.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 97%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -MF CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o.d -o CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -3573,6 +3612,24 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 97%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -MF CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o.d -o CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 97%] Built target vcfindex +make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 97%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -MF CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o.d -o CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfinfo2qual.cpp +In file included from /usr/include/c++/12/queue:62, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:23: +/usr/include/c++/12/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++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -3589,36 +3646,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/queue:62, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:23: -/usr/include/c++/12/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++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -[ 97%] Linking CXX executable vcf2dag -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 97%] Built target vcf2dag -make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 97%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -MF CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o.d -o CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfinfo2qual.cpp -In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp:194:31: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfinfo2qual.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -3635,31 +3662,52 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp:194:31: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 97%] Linking CXX executable vcfsample2info +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 97%] Linking CXX executable vcf2dag +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 97%] Built target vcfsample2info +make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend [ 97%] Linking CXX executable vcfqual2info /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfqual2info.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 97%] Built target vcfqual2info -make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglbound.dir/DependInfo.cmake --color= +[ 98%] Linking CXX executable vcfinfo2qual +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfo2qual.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 97%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o +[ 98%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -MF CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o.d -o CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp -[ 97%] Linking CXX executable vcfsample2info -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 97%] Built target vcfsample2info +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' +[ 98%] Built target vcf2dag make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake --color= +[ 98%] Built target vcfqual2info +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 97%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o +[ 98%] Built target vcfinfo2qual +[ 98%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -MF CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o.d -o CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfinfosummarize.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -3693,11 +3741,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable vcfinfo2qual -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfo2qual.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' -[ 98%] Built target vcfinfo2qual In file included from /usr/include/c++/12/queue:62, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:23: /usr/include/c++/12/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]': @@ -3720,15 +3763,15 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 99%] Linking CXX executable vcfglbound +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglbound.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfinfosummarize.cpp:204:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 99%] Linking CXX executable vcfglbound -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglbound.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 99%] Built target vcfglbound [100%] Linking CXX executable vcfinfosummarize @@ -3769,22 +3812,22 @@ [----------] Global test environment set-up. [----------] 1 test from Variant [ RUN ] Variant.correctGenotype -[ OK ] Variant.correctGenotype (19341 ms) -[----------] 1 test from Variant (19341 ms total) +[ OK ] Variant.correctGenotype (6613 ms) +[----------] 1 test from Variant (6613 ms total) [----------] 4 tests from VariantCallFile [ RUN ] VariantCallFile.open -[ OK ] VariantCallFile.open (4 ms) +[ OK ] VariantCallFile.open (1 ms) [ RUN ] VariantCallFile.recordCountUncompressed -[ OK ] VariantCallFile.recordCountUncompressed (1 ms) +[ OK ] VariantCallFile.recordCountUncompressed (0 ms) [ RUN ] VariantCallFile.recordCountCompressed -[ OK ] VariantCallFile.recordCountCompressed (43 ms) +[ OK ] VariantCallFile.recordCountCompressed (13 ms) [ RUN ] VariantCallFile.sampleNamesCompressed -[ OK ] VariantCallFile.sampleNamesCompressed (19 ms) -[----------] 4 tests from VariantCallFile (69 ms total) +[ OK ] VariantCallFile.sampleNamesCompressed (5 ms) +[----------] 4 tests from VariantCallFile (21 ms total) [----------] Global test environment tear-down -[==========] 5 tests from 2 test suites ran. (19411 ms total) +[==========] 5 tests from 2 test suites ran. (6635 ms total) [ PASSED ] 5 tests. make[2]: Leaving directory '/build/libvcflib-1.0.3+dfsg/test' make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' @@ -3792,7 +3835,7 @@ dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/libvcflib-1.0.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/libvcflib-1.0.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libvcflib-1.0.3+dfsg -B/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -4026,91 +4069,91 @@ -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/vec128int.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/veclib_types.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcffilter.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgeno2alleles.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfallelicprimitives.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/pVst.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfparsealts.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfannotategenotypes.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepgeno.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfevenregions.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfld.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/plotHaps.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfbreakmulti.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcreatemulti.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfaddinfo.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfstats.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/segmentIhs.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenosummarize.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcflength.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfuniq.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcountalleles.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/pVst.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepsamples.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgeno2alleles.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/pFst.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsample2info.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/smoother.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfglbound.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgeno2haplo.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/bFst.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfafpath.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcommonsamples.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfecho.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfintersect.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcffixup.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenosamplenames.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepinfo.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfuniqalleles.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/pFst.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/iHS.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/sequenceDiversity.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/permuteGPAT++.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfhethomratio.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfstreamsort.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfglxgt.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfindex.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfentropy.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/meltEHH.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/normalize-iHS.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/wcFst.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcombine.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfintersect.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsamplediff.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenotypes.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfnulldotslashdot.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2tsv.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfdistance.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfroc.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/hapLrt.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/segmentFst.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfrandom.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcheck.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcffixup.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/smoother.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfremovesamples.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/dumpContigsFromHeader.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgeno2haplo.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfhetcount.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfflatten.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfld.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/normalize-iHS.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/sequenceDiversity.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfnumalt.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfecho.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfinfo2qual.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfallelicprimitives.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepinfo.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfaltcount.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsample2info.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfindex.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/bFst.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfleftalign.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/genotypeSummary.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfqual2info.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfparsealts.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfremovesamples.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfstats.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenosummarize.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfremoveaberrantgenotypes.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfleftalign.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcleancomplex.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfuniq.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcountalleles.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfoverlay.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/abba-baba.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/popStats.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepsamples.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2dag.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenotypecompare.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcombine.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/segmentFst.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcreatemulti.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfannotate.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfhethomratio.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfglbound.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/permuteSmooth.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfaddinfo.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfannotategenotypes.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfrandomsample.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfprimers.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcflib.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfclassify.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2fasta.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfremap.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/iHS.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfoverlay.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/genotypeSummary.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfdistance.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/permuteSmooth.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsamplenames.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfinfosummarize.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfbreakmulti.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfclassify.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfflatten.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcat.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcleancomplex.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/segmentIhs.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfglxgt.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfroc.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfentropy.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/permuteGPAT++.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfnumalt.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/popStats.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsamplediff.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenosamplenames.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenotypes.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcffilter.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/abba-baba.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfrandom.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/meltEHH.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfuniqalleles.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfevenregions.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsamplenames.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfstreamsort.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepgeno.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/hapLrt.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfnulldotslashdot.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfaltcount.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfremoveaberrantgenotypes.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenotypecompare.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcommonsamples.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcflib.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfrandomsample.1 +-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfhetcount.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsitesummarize.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2tsv.1 --- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2fasta.1 make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' debian/rules override_dh_install make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' @@ -4156,104 +4199,104 @@ 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/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/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/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/segmentFst 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/vcfevenregions 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/permuteGPAT++ 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/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/permuteSmooth 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/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/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/genotypeSummary 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/vcfintersect 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/vcfhethomratio 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/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/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/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/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/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/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/vcf2dag 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/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/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/smoother 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/abba-baba 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/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/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/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/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/vcfcleancomplex 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/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/vcfglbound 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/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/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/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/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/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/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/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/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/permuteGPAT++ 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/vcfentropy 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/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/vcfhetcount 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/vcfgenotypecompare 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/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/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/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/vcfaltcount 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/vcfentropy 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/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/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/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/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/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/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/vcfinfosummarize 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/vcfinfo2qual 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/permuteSmooth 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/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/dumpContigsFromHeader 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/meltEHH 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/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/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/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/vcfgenotypecompare 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/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/vcfcleancomplex 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/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/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/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/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/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/smoother 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/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/vcf2fasta 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/meltEHH 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/segmentFst 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/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/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/segmentIhs 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/vcfintersect 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/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/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/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/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/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/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/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/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/vcfhethomratio 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/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/vcfparsealts 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/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/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/vcfafpath 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/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/abba-baba 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/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/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/plotHaps 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/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/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/genotypeSummary 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/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/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/vcf2fasta 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/vcfinfosummarize 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/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/lib/vcflib/bin/vcfparsealts 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 +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/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/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/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/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/plotHaps 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/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/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/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/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/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/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/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/lib/vcflib/bin/vcfinfo2qual 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/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/vcfhetcount 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/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/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/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/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/vcfglbound 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 dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: package libvcflib-tools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package libvcflib-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake +dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.3+dfsg-2_armhf.deb'. dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.3+dfsg-2_armhf.deb'. dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.3+dfsg-2_armhf.deb'. -dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.3+dfsg-2_armhf.deb'. dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.3+dfsg-2_armhf.deb'. dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.3+dfsg-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../libvcflib_1.0.3+dfsg-2_armhf.buildinfo @@ -4263,12 +4306,14 @@ 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/6484/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/6484/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/10593 and its subdirectories -I: Current time: Tue May 30 20:01:02 -12 2023 -I: pbuilder-time-stamp: 1685520062 +I: removing directory /srv/workspace/pbuilder/6484 and its subdirectories +I: Current time: Wed May 31 22:13:12 +14 2023 +I: pbuilder-time-stamp: 1685520792