Diff of the two buildlogs: -- --- b1/build.log 2021-09-07 03:27:21.691389282 +0000 +++ b2/build.log 2021-09-07 03:42:33.202638442 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 6 15:01:03 -12 2021 -I: pbuilder-time-stamp: 1630983663 +I: Current time: Tue Sep 7 17:28:08 +14 2021 +I: pbuilder-time-stamp: 1630985288 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./hinge_0.5.0-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.ENUS5krU/trustedkeys.kbx': General error -gpgv: Signature made Thu Mar 19 05:26:36 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.salox8hM/trustedkeys.kbx': General error +gpgv: Signature made Fri Mar 20 07:26:36 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -33,135 +33,169 @@ dpkg-source: info: applying spdlog-1.5.0.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/14251/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1146/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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1146/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1146/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='821cfbd6c1914c3e91e2126f5343ebf5' - 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='14251' - PS1='# ' - PS2='> ' + INVOCATION_ID=ae4c7545ac584049b5d52688e3d0459d + 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=1146 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.0krsq1DqMF/pbuilderrc_fNrB --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.0krsq1DqMF/b1 --logfile b1/build.log hinge_0.5.0-6.dsc' - SUDO_GID='116' - SUDO_UID='112' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.0krsq1DqMF/pbuilderrc_bNVf --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.0krsq1DqMF/b2 --logfile b2/build.log hinge_0.5.0-6.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux cbxi4b 5.10.0-8-armmp #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more - -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 20 21:28 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 2021 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/14251/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more + -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 7 17:28 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 21 23:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 2021 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/1146/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -383,7 +417,7 @@ Get: 150 http://deb.debian.org/debian bullseye/main armhf python3-pysam armhf 0.15.4+ds-3+b2 [1381 kB] Get: 151 http://deb.debian.org/debian bullseye/main armhf python3-pbcore all 1.7.1+git20200430.a127b1e+dfsg-1 [2881 kB] Get: 152 http://deb.debian.org/debian bullseye/main armhf python3-ujson armhf 4.0.2-1 [19.9 kB] -Fetched 103 MB in 45s (2307 kB/s) +Fetched 103 MB in 39s (2666 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) @@ -1012,7 +1046,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/hinge-0.5.0/ && 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 > ../hinge_0.5.0-6_source.changes +hostname: Name or service not known +I: Running cd /build/hinge-0.5.0/ && 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 > ../hinge_0.5.0-6_source.changes dpkg-buildpackage: info: source package hinge dpkg-buildpackage: info: source version 0.5.0-6 dpkg-buildpackage: info: source distribution unstable @@ -1056,50 +1091,56 @@ -- Build files have been written to: /build/hinge-0.5.0/obj-arm-linux-gnueabihf 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[1]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/hinge-0.5.0 -B/build/hinge-0.5.0/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-arm-linux-gnueabihf/CMakeFiles /build/hinge-0.5.0/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/depend -make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/CMakeFiles/man.dir/DependInfo.cmake --color= -make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend +make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake --color= +make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake --color= -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/ini.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/ini.dir/depend.internal". -Scanning dependencies of target ini -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake --color= Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/CMakeFiles/man.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/CMakeFiles/man.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/CMakeFiles/man.dir/depend.internal". Scanning dependencies of target man -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DB.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DB.dir/depend.internal". make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DB.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DB.dir/depend.internal". Scanning dependencies of target DB -[ 3%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/ini.dir/ini.c.o -c /build/hinge-0.5.0/src/lib/ini.c make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/ini.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/ini.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/depend.internal". +Scanning dependencies of target PAF +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build +Scanning dependencies of target ini +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build +[ 3%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o [ 6%] Generating hinge.1 +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin && /usr/bin/pandoc --from markdown --to man -s /build/hinge-0.5.0/src/hinge.1.md -o hinge.1 -[ 10%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DB.dir/DB.c.o -c /build/hinge-0.5.0/src/lib/DB.c -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 10%] Built target man -make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake --color= +[ 10%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/PAF.dir/paf.c.o -c /build/hinge-0.5.0/src/lib/paf.c +[ 13%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/ini.dir/ini.c.o -c /build/hinge-0.5.0/src/lib/ini.c /build/hinge-0.5.0/src/lib/DB.c: In function 'Load_QVs': /build/hinge-0.5.0/src/lib/DB.c:916:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 916 | fscanf(istub,DB_NFILE,&nfiles); @@ -1110,51 +1151,28 @@ /build/hinge-0.5.0/src/lib/DB.c:925:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 925 | { fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/depend.internal". -Scanning dependencies of target PAF make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 13%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/PAF.dir/paf.c.o -c /build/hinge-0.5.0/src/lib/paf.c -[ 17%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/c++ -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/hinge-0.5.0/src/lib/INIReader.cpp -[ 20%] Linking C static library libPAF.a -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1 -/usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o -/usr/bin/ranlib libPAF.a -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 20%] Built target PAF +[ 13%] Built target man make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake --color= +[ 17%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/c++ -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/hinge-0.5.0/src/lib/INIReader.cpp Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/LA.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/LA.dir/depend.internal". Scanning dependencies of target LA make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 20%] Linking C static library libPAF.a +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake [ 24%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/LA.dir/align.c.o -c /build/hinge-0.5.0/src/lib/align.c -[ 27%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DB.dir/QV.c.o -c /build/hinge-0.5.0/src/lib/QV.c -/build/hinge-0.5.0/src/lib/QV.c: In function 'Build_Table': -/build/hinge-0.5.0/src/lib/QV.c:164:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 164 | { uint64 symbol = (uint64) (node->lft); - | ^ -/build/hinge-0.5.0/src/lib/QV.c: In function 'Huffman': -/build/hinge-0.5.0/src/lib/QV.c:211:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 211 | node[value].lft = (HTree *) (uint64) i; - | ^ -[ 31%] Linking CXX static library libini.a -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/ini.dir/cmake_clean_target.cmake -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/ini.dir/link.txt --verbose=1 -/usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o -/usr/bin/ranlib libini.a +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1 +/usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o +/usr/bin/ranlib libPAF.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 31%] Built target ini +[ 24%] Built target PAF make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake --color= @@ -1164,7 +1182,7 @@ make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 34%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o +[ 27%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -c /build/hinge-0.5.0/src/lib/kmer_lookup.c /build/hinge-0.5.0/src/lib/kmer_lookup.c: In function 'find_best_aln_range': /build/hinge-0.5.0/src/lib/kmer_lookup.c:347:14: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] @@ -1181,13 +1199,13 @@ /usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ -[ 37%] Linking C static library libkmer_lookup.a +[ 31%] Linking C static library libkmer_lookup.a cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kmer_lookup.dir/link.txt --verbose=1 /usr/bin/ar qc libkmer_lookup.a CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o /usr/bin/ranlib libkmer_lookup.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 37%] Built target kmer_lookup +[ 31%] Built target kmer_lookup make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake --color= @@ -1197,40 +1215,57 @@ make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 41%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o +[ 34%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/hinge-0.5.0/src/lib/DW_banded.c -[ 44%] Linking C static library libDB.a -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 -/usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o -/usr/bin/ranlib libDB.a -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 44%] Built target DB -[ 48%] Linking C static library libDW_banded.a +[ 37%] Linking C static library libDW_banded.a cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DW_banded.dir/link.txt --verbose=1 /usr/bin/ar qc libDW_banded.a CMakeFiles/DW_banded.dir/DW_banded.c.o /usr/bin/ranlib libDW_banded.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 48%] Built target DW_banded +[ 37%] Built target DW_banded make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake --color= +[ 41%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DB.dir/QV.c.o -c /build/hinge-0.5.0/src/lib/QV.c Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/falcon.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/falcon.dir/depend.internal". Scanning dependencies of target falcon make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 51%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o +[ 44%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/falcon.dir/falcon.c.o -c /build/hinge-0.5.0/src/lib/falcon.c -[ 55%] Linking C static library libfalcon.a +/build/hinge-0.5.0/src/lib/QV.c: In function 'Build_Table': +/build/hinge-0.5.0/src/lib/QV.c:164:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 164 | { uint64 symbol = (uint64) (node->lft); + | ^ +/build/hinge-0.5.0/src/lib/QV.c: In function 'Huffman': +/build/hinge-0.5.0/src/lib/QV.c:211:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 211 | node[value].lft = (HTree *) (uint64) i; + | ^ +[ 48%] Linking C static library libfalcon.a cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1 /usr/bin/ar qc libfalcon.a CMakeFiles/falcon.dir/falcon.c.o /usr/bin/ranlib libfalcon.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 55%] Built target falcon +[ 48%] Built target falcon +[ 51%] Linking CXX static library libini.a +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/ini.dir/cmake_clean_target.cmake +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/ini.dir/link.txt --verbose=1 +/usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o +/usr/bin/ranlib libini.a +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 51%] Built target ini +[ 55%] Linking C static library libDB.a +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 +/usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o +/usr/bin/ranlib libDB.a +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 55%] Built target DB [ 58%] Linking C static library libLA.a cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/LA.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/LA.dir/link.txt --verbose=1 @@ -1275,38 +1310,49 @@ make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' [ 65%] Built target LAInterface make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/depend -make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/filter /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake --color= -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend +make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/maximal /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake --color= -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/consensus.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/consensus.dir/depend.internal". -Scanning dependencies of target consensus -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build +make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake --color= Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter/CMakeFiles/Reads_filter.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter/CMakeFiles/Reads_filter.dir/depend.internal". -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/draft_assembly.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/draft_assembly.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal/CMakeFiles/get_maximal_reads.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal/CMakeFiles/get_maximal_reads.dir/depend.internal". Scanning dependencies of target Reads_filter make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build +Scanning dependencies of target draft_assembly +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' Scanning dependencies of target get_maximal_reads +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/consensus.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/consensus.dir/depend.internal". make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build +Scanning dependencies of target consensus +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 68%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/hinge-0.5.0/src/consensus/consensus.cpp -[ 72%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -[ 75%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/hinge-0.5.0/src/maximal/maximal.cpp +make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 68%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/hinge-0.5.0/src/filter/filter.cpp +[ 72%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/hinge-0.5.0/src/maximal/maximal.cpp +[ 75%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/hinge-0.5.0/src/consensus/draft.cpp +[ 79%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/hinge-0.5.0/src/consensus/consensus.cpp /build/hinge-0.5.0/src/consensus/consensus.cpp: In function 'int main(int, char**)': /build/hinge-0.5.0/src/consensus/consensus.cpp:126:15: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 126 | printf("%lu\n", res.size()); @@ -1321,22 +1367,22 @@ | | | | long unsigned int std::vector::size_type {aka unsigned int} | %u -[ 79%] Linking CXX executable consensus +[ 82%] Linking CXX executable consensus cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/consensus.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/consensus.dir/consensus.cpp.o -o consensus -lfmt ../lib/libLAInterface.a ../lib/libfalcon.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 79%] Built target consensus -make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend +[ 82%] Built target consensus +make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake --color= -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/draft_assembly.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/draft_assembly.dir/depend.internal". -Scanning dependencies of target draft_assembly +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/layout /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake --color= +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/hinging.dir/depend.internal". +Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/hinging.dir/depend.internal". +Scanning dependencies of target hinging make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build +make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 82%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/hinge-0.5.0/src/consensus/draft.cpp +[ 86%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/hinge-0.5.0/src/layout/hinging.cpp /build/hinge-0.5.0/src/consensus/draft.cpp: In function 'int draft_assembly_ctg(std::vector >&, LAInterface&, std::vector&, std::unordered_map >&, std::unordered_map > >&, std::vector&, int, int, int, int, int, bool, bool, std::string&)': /build/hinge-0.5.0/src/consensus/draft.cpp:514:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector > >::size_type' {aka 'unsigned int'} [-Wformat=] 514 | printf("In total %lu lanes\n", lanes.size()); @@ -1344,22 +1390,11 @@ | | | | long unsigned int std::vector > >::size_type {aka unsigned int} | %u -[ 86%] Linking CXX executable get_maximal_reads +[ 89%] Linking CXX executable get_maximal_reads cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal && /usr/bin/cmake -E cmake_link_script CMakeFiles/get_maximal_reads.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -o get_maximal_reads -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 86%] Built target get_maximal_reads -make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/layout /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake --color= -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/hinging.dir/depend.internal". -Dependee "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/hinging.dir/depend.internal". -Scanning dependencies of target hinging -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 89%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/hinge-0.5.0/src/layout/hinging.cpp +[ 89%] Built target get_maximal_reads [ 93%] Linking CXX executable Reads_filter cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/Reads_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Reads_filter.dir/filter.cpp.o -o Reads_filter -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz @@ -1382,99 +1417,111 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/hinge-0.5.0 -B/build/hinge-0.5.0/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-arm-linux-gnueabihf/CMakeFiles /build/hinge-0.5.0/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/depend -make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend -make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/CMakeFiles/man.dir/DependInfo.cmake --color= +make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake --color= +make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake --color= +make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'bin/CMakeFiles/man.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make[3]: Nothing to be done for 'bin/lib/CMakeFiles/DB.dir/build'. -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/ini.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' [ 3%] Built target man -make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend -[ 13%] Built target DB make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake --color= -[ 24%] Built target ini -make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build -make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build +make[3]: Nothing to be done for 'bin/lib/CMakeFiles/DB.dir/build'. +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/PAF.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 13%] Built target ini +make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake --color= +make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/LA.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 24%] Built target DB +[ 31%] Built target PAF +make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build -[ 31%] Built target PAF make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/kmer_lookup.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend [ 37%] Built target LA -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake --color= make -f bin/lib/CMakeFiles/LAInterface.dir/build.make bin/lib/CMakeFiles/LAInterface.dir/depend +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/LAInterface.dir/DependInfo.cmake --color= +make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build [ 44%] Built target kmer_lookup +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make[3]: Nothing to be done for 'bin/lib/CMakeFiles/DW_banded.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 51%] Built target DW_banded +make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/depend +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake --color= make -f bin/lib/CMakeFiles/LAInterface.dir/build.make bin/lib/CMakeFiles/LAInterface.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/LAInterface.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build +[ 58%] Built target LAInterface +make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make[3]: Nothing to be done for 'bin/lib/CMakeFiles/DW_banded.dir/build'. +make[3]: Nothing to be done for 'bin/lib/CMakeFiles/falcon.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 51%] Built target LAInterface make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/depend make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/filter /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake --color= -[ 58%] Built target DW_banded make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/maximal /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake --color= make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/maximal /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake --color= cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/layout /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake --color= +[ 65%] Built target falcon +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend +make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' +cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'bin/filter/CMakeFiles/Reads_filter.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'bin/maximal/CMakeFiles/get_maximal_reads.dir/build'. @@ -1484,36 +1531,24 @@ make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'bin/layout/CMakeFiles/hinging.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 65%] Built target Reads_filter -[ 72%] Built target get_maximal_reads -make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/depend -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake --color= -[ 79%] Built target hinging -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/build -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make[3]: Nothing to be done for 'bin/lib/CMakeFiles/falcon.dir/build'. +[ 72%] Built target Reads_filter make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 86%] Built target falcon -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build +[ 79%] Built target get_maximal_reads make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'bin/consensus/CMakeFiles/consensus.dir/build'. +make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus /build/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build +[ 86%] Built target hinging +[ 93%] Built target consensus make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make[3]: Nothing to be done for 'bin/consensus/CMakeFiles/consensus.dir/build'. -make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' -make[3]: Entering directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'bin/consensus/CMakeFiles/draft_assembly.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' [100%] Built target draft_assembly -[100%] Built target consensus make[2]: Leaving directory '/build/hinge-0.5.0/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-arm-linux-gnueabihf/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall @@ -1524,61 +1559,61 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_bandage_file.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_alignment.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region_find_bridges.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_annotate_clip_ends.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_w_repeat.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/fasta_to_fastq.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth_json.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping2.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/clip_ends.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/merge_hinges.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_read.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_alignment.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus_norevcomp.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region_find_bridges.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/unitig.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph_nogt.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/random_condensation.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping3.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_read.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping_nanopore.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/Visualise_graph.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw.sh +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping3.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/clip_ends.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph_nogt.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/split_las.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/repeat_annotate_reads.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_alignment.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pileup.ipynb +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping_nanopore.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/connected.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_annotate_clip_ends.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_alignment.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_annotation.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/Visualise_graph.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_read.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path_norevcomp.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_bandage_file.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_annotation.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/random_condensation.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/unitig.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus_norevcomp.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_consensus_gfa.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/split_las.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_w_repeat.py --- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw.sh +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping2.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh +-- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/share/man/man1/hinge.1 -- Installing: /build/hinge-0.5.0/debian/hinge/usr/bin/hinge -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/Reads_filter @@ -1608,17 +1643,17 @@ dh_strip dh_makeshlibs dh_shlibdeps -dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/Reads_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/consensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/get_maximal_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/draft_assembly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/consensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/hinging contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/get_maximal_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/Reads_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'hinge-dbgsym' in '../hinge-dbgsym_0.5.0-6_armhf.deb'. dpkg-deb: building package 'hinge' in '../hinge_0.5.0-6_armhf.deb'. +dpkg-deb: building package 'hinge-dbgsym' in '../hinge-dbgsym_0.5.0-6_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../hinge_0.5.0-6_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1626,12 +1661,14 @@ 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/1146/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1146/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/14251 and its subdirectories -I: Current time: Mon Sep 6 15:27:16 -12 2021 -I: pbuilder-time-stamp: 1630985236 +I: removing directory /srv/workspace/pbuilder/1146 and its subdirectories +I: Current time: Tue Sep 7 17:42:29 +14 2021 +I: pbuilder-time-stamp: 1630986149