I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 13 01:38:37 +14 2021 I: pbuilder-time-stamp: 1628768317 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [jellyfish_2.3.0-10.dsc] I: copying [./jellyfish_2.3.0.orig.tar.gz] I: copying [./jellyfish_2.3.0-10.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.MpLDR1oX/trustedkeys.kbx': General error gpgv: Signature made Wed Mar 3 02:19:08 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./jellyfish_2.3.0-10.dsc dpkg-source: info: extracting jellyfish in jellyfish-2.3.0 dpkg-source: info: unpacking jellyfish_2.3.0.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.3.0-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying manpage_whatis_entry.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying fix_replacement_of_-L_option.patch dpkg-source: info: applying test_needs_bash dpkg-source: info: applying python3 dpkg-source: info: applying fix-32-bit.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/14891/tmp/hooks/D01_modify_environment starting debug: Running on virt64b. 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/14891/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/14891/tmp/hooks/D02_print_environment starting I: set 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=3be7c7ff803f4727ae34face2f320ff4 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=14891 PS4='+ ' 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.gP121BBc9l/pbuilderrc_Lii3 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.gP121BBc9l/b2 --logfile b2/build.log --extrapackages usrmerge jellyfish_2.3.0-10.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 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 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 06:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln -rwxr-xr-x 1 root root 35068 Feb 8 2020 login -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls -rwxr-xr-x 1 root root 99940 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 Aug 13 01:38 sh -> bash lrwxrwxrwx 1 root root 4 Aug 11 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 23:55 tar -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch -rwxr-xr-x 1 root root 22496 Sep 23 2020 true -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 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 13:30 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 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/14891/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19398 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on yaggo; however: Package yaggo is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on time; however: Package time is not installed. pbuilder-satisfydepends-dummy depends on procps; however: Package procps is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on dos2unix; however: Package dos2unix is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bsdextrautils{a} ca-certificates{a} chrpath{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dos2unix{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libhts-dev{a} libhts3{a} libicu67{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps8{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libruby2.7{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} openssl{a} pkg-config{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.9{a} python3.9-dev{a} python3.9-minimal{a} rake{a} readline-common{a} ruby{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.7{a} rubygems-integration{a} samtools{a} sensible-utils{a} swig{a} swig4.0{a} time{a} yaggo{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato javascript-common libarchive-cpio-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 105 newly installed, 0 to remove and 0 not upgraded. Need to get 46.3 MB of archives. After unpacking 145 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf libpython3.9-minimal armhf 3.9.2-1 [790 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libexpat1 armhf 2.2.10-2 [76.3 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf python3.9-minimal armhf 3.9.2-1 [1630 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libmpdec3 armhf 2.5.1-1 [74.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf libreadline8 armhf 8.1-1 [147 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf libpython3.9-stdlib armhf 3.9.2-1 [1608 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf python3.9 armhf 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf python3 armhf 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libncurses6 armhf 6.2+20201114-2 [80.5 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf libprocps8 armhf 2:3.3.17-5 [60.7 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf procps armhf 2:3.3.17-5 [492 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf openssl armhf 1.1.1k-1 [826 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf ca-certificates all 20210119 [158 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf bc armhf 1.07.1-2+b2 [104 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf chrpath armhf 0.16-2+b1 [15.9 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf d-shlibs all 0.98 [17.9 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf python3-distutils all 3.9.2-1 [143 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf dh-python all 4.20201102+nmu1 [99.4 kB] Get: 55 http://deb.debian.org/debian bullseye/main armhf dos2unix armhf 7.4.1-1 [389 kB] Get: 56 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf libmd0 armhf 1.0.3-3 [27.4 kB] Get: 58 http://deb.debian.org/debian bullseye/main armhf libbsd0 armhf 0.11.3-1 [103 kB] Get: 59 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1 [67.6 kB] Get: 60 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1 [99.1 kB] Get: 61 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3 [210 kB] Get: 62 http://deb.debian.org/debian bullseye/main armhf libnghttp2-14 armhf 1.43.0-1 [65.6 kB] Get: 63 http://deb.debian.org/debian bullseye/main armhf libpsl5 armhf 0.21.0-1.2 [56.1 kB] Get: 64 http://deb.debian.org/debian bullseye/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 65 http://deb.debian.org/debian bullseye/main armhf libssh2-1 armhf 1.9.0-2 [143 kB] Get: 66 http://deb.debian.org/debian bullseye/main armhf libcurl3-gnutls armhf 7.74.0-1.3+b1 [306 kB] Get: 67 http://deb.debian.org/debian bullseye/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3+b1 [402 kB] Get: 68 http://deb.debian.org/debian bullseye/main armhf libdeflate0 armhf 1.7-1 [43.1 kB] Get: 69 http://deb.debian.org/debian bullseye/main armhf libdeflate-dev armhf 1.7-1 [39.9 kB] Get: 70 http://deb.debian.org/debian bullseye/main armhf libedit2 armhf 3.1-20191231-2+b1 [81.1 kB] Get: 71 http://deb.debian.org/debian bullseye/main armhf libexpat1-dev armhf 2.2.10-2 [123 kB] Get: 72 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB] Get: 73 http://deb.debian.org/debian bullseye/main armhf libhts3 armhf 1.11-4 [332 kB] Get: 74 http://deb.debian.org/debian bullseye/main armhf liblzma-dev armhf 5.2.5-2 [220 kB] Get: 75 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] Get: 76 http://deb.debian.org/debian bullseye/main armhf libhts-dev armhf 1.11-4 [3819 kB] Get: 77 http://deb.debian.org/debian bullseye/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 78 http://deb.debian.org/debian bullseye/main armhf libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 79 http://deb.debian.org/debian bullseye/main armhf libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 80 http://deb.debian.org/debian bullseye/main armhf libpython3.9 armhf 3.9.2-1 [1447 kB] Get: 81 http://deb.debian.org/debian bullseye/main armhf libpython3.9-dev armhf 3.9.2-1 [3160 kB] Get: 82 http://deb.debian.org/debian bullseye/main armhf libpython3-dev armhf 3.9.2-3 [21.7 kB] Get: 83 http://deb.debian.org/debian bullseye/main armhf libpython3-all-dev armhf 3.9.2-3 [1068 B] Get: 84 http://deb.debian.org/debian bullseye/main armhf rubygems-integration all 1.18 [6704 B] Get: 85 http://deb.debian.org/debian bullseye/main armhf ruby2.7 armhf 2.7.4-1 [747 kB] Get: 86 http://deb.debian.org/debian bullseye/main armhf ruby-rubygems all 3.2.5-2 [281 kB] Get: 87 http://deb.debian.org/debian bullseye/main armhf ruby armhf 1:2.7+2 [11.7 kB] Get: 88 http://deb.debian.org/debian bullseye/main armhf rake all 13.0.3-1 [84.7 kB] Get: 89 http://deb.debian.org/debian bullseye/main armhf ruby-minitest all 5.13.0-1 [57.3 kB] Get: 90 http://deb.debian.org/debian bullseye/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 91 http://deb.debian.org/debian bullseye/main armhf ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 92 http://deb.debian.org/debian bullseye/main armhf ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 93 http://deb.debian.org/debian bullseye/main armhf ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 94 http://deb.debian.org/debian bullseye/main armhf libyaml-0-2 armhf 0.2.2-1 [42.0 kB] Get: 95 http://deb.debian.org/debian bullseye/main armhf libruby2.7 armhf 2.7.4-1 [3956 kB] Get: 96 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] Get: 97 http://deb.debian.org/debian bullseye/main armhf python3-all armhf 3.9.2-3 [1056 B] Get: 98 http://deb.debian.org/debian bullseye/main armhf python3.9-dev armhf 3.9.2-1 [515 kB] Get: 99 http://deb.debian.org/debian bullseye/main armhf python3-dev armhf 3.9.2-3 [24.8 kB] Get: 100 http://deb.debian.org/debian bullseye/main armhf python3-all-dev armhf 3.9.2-3 [1064 B] Get: 101 http://deb.debian.org/debian bullseye/main armhf samtools armhf 1.11-1 [519 kB] Get: 102 http://deb.debian.org/debian bullseye/main armhf swig4.0 armhf 4.0.2-1 [1327 kB] Get: 103 http://deb.debian.org/debian bullseye/main armhf swig all 4.0.2-1 [330 kB] Get: 104 http://deb.debian.org/debian bullseye/main armhf time armhf 1.9-0.1 [50.8 kB] Get: 105 http://deb.debian.org/debian bullseye/main armhf yaggo all 1.5.10-2 [18.9 kB] Fetched 46.3 MB in 8s (5775 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.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_armhf.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../1-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../3-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:armhf. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_armhf.deb ... Unpacking libpython3.9-minimal:armhf (3.9.2-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../6-libexpat1_2.2.10-2_armhf.deb ... Unpacking libexpat1:armhf (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_armhf.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:armhf (3.9.2-1) ... Setting up libexpat1:armhf (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 20265 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_armhf.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:armhf. Preparing to unpack .../2-libmpdec3_2.5.1-1_armhf.deb ... Unpacking libmpdec3:armhf (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:armhf. Preparing to unpack .../4-libreadline8_8.1-1_armhf.deb ... Unpacking libreadline8:armhf (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:armhf. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_armhf.deb ... Unpacking libpython3.9-stdlib:armhf (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_armhf.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (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 ... 20686 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_armhf.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../01-libncurses6_6.2+20201114-2_armhf.deb ... Unpacking libncurses6:armhf (6.2+20201114-2) ... Selecting previously unselected package libprocps8:armhf. Preparing to unpack .../02-libprocps8_2%3a3.3.17-5_armhf.deb ... Unpacking libprocps8:armhf (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../03-procps_2%3a3.3.17-5_armhf.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../04-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../05-openssl_1.1.1k-1_armhf.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../06-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.39-3_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../08-libmagic1_1%3a5.39-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.39-3_armhf.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../11-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package bc. Preparing to unpack .../17-bc_1.07.1-2+b2_armhf.deb ... Unpacking bc (1.07.1-2+b2) ... Selecting previously unselected package chrpath. Preparing to unpack .../18-chrpath_0.16-2+b1_armhf.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../19-d-shlibs_0.98_all.deb ... Unpacking d-shlibs (0.98) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../20-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../21-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../22-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../23-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../24-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../25-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../26-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../27-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../28-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../29-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../30-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../31-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../32-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../33-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../34-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../35-python3-lib2to3_3.9.2-1_all.deb ... Unpacking python3-lib2to3 (3.9.2-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../36-python3-distutils_3.9.2-1_all.deb ... Unpacking python3-distutils (3.9.2-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../37-dh-python_4.20201102+nmu1_all.deb ... Unpacking dh-python (4.20201102+nmu1) ... Selecting previously unselected package dos2unix. Preparing to unpack .../38-dos2unix_7.4.1-1_armhf.deb ... Unpacking dos2unix (7.4.1-1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../39-libbrotli1_1.0.9-2+b2_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b2) ... Selecting previously unselected package libmd0:armhf. Preparing to unpack .../40-libmd0_1.0.3-3_armhf.deb ... Unpacking libmd0:armhf (1.0.3-3) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../41-libbsd0_0.11.3-1_armhf.deb ... Unpacking libbsd0:armhf (0.11.3-1) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../42-libsasl2-modules-db_2.1.27+dfsg-2.1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../43-libsasl2-2_2.1.27+dfsg-2.1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:armhf. Preparing to unpack .../44-libldap-2.4-2_2.4.57+dfsg-3_armhf.deb ... Unpacking libldap-2.4-2:armhf (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../45-libnghttp2-14_1.43.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.43.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../46-libpsl5_0.21.0-1.2_armhf.deb ... Unpacking libpsl5:armhf (0.21.0-1.2) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../47-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../48-libssh2-1_1.9.0-2_armhf.deb ... Unpacking libssh2-1:armhf (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../49-libcurl3-gnutls_7.74.0-1.3+b1_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.74.0-1.3+b1) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../50-libcurl4-gnutls-dev_7.74.0-1.3+b1_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (7.74.0-1.3+b1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../51-libdeflate0_1.7-1_armhf.deb ... Unpacking libdeflate0:armhf (1.7-1) ... Selecting previously unselected package libdeflate-dev:armhf. Preparing to unpack .../52-libdeflate-dev_1.7-1_armhf.deb ... Unpacking libdeflate-dev:armhf (1.7-1) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../53-libedit2_3.1-20191231-2+b1_armhf.deb ... Unpacking libedit2:armhf (3.1-20191231-2+b1) ... Selecting previously unselected package libexpat1-dev:armhf. Preparing to unpack .../54-libexpat1-dev_2.2.10-2_armhf.deb ... Unpacking libexpat1-dev:armhf (2.2.10-2) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../55-libglib2.0-0_2.66.8-1_armhf.deb ... Unpacking libglib2.0-0:armhf (2.66.8-1) ... Selecting previously unselected package libhts3:armhf. Preparing to unpack .../56-libhts3_1.11-4_armhf.deb ... Unpacking libhts3:armhf (1.11-4) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../57-liblzma-dev_5.2.5-2_armhf.deb ... Unpacking liblzma-dev:armhf (5.2.5-2) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../58-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../59-libhts-dev_1.11-4_armhf.deb ... Unpacking libhts-dev:armhf (1.11-4) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../60-libjs-jquery_3.5.1+dfsg+~3.5.5-7_all.deb ... Unpacking libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../61-libjs-underscore_1.9.1~dfsg-3_all.deb ... Unpacking libjs-underscore (1.9.1~dfsg-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../62-libjs-sphinxdoc_3.4.3-2_all.deb ... Unpacking libjs-sphinxdoc (3.4.3-2) ... Selecting previously unselected package libpython3.9:armhf. Preparing to unpack .../63-libpython3.9_3.9.2-1_armhf.deb ... Unpacking libpython3.9:armhf (3.9.2-1) ... Selecting previously unselected package libpython3.9-dev:armhf. Preparing to unpack .../64-libpython3.9-dev_3.9.2-1_armhf.deb ... Unpacking libpython3.9-dev:armhf (3.9.2-1) ... Selecting previously unselected package libpython3-dev:armhf. Preparing to unpack .../65-libpython3-dev_3.9.2-3_armhf.deb ... Unpacking libpython3-dev:armhf (3.9.2-3) ... Selecting previously unselected package libpython3-all-dev:armhf. Preparing to unpack .../66-libpython3-all-dev_3.9.2-3_armhf.deb ... Unpacking libpython3-all-dev:armhf (3.9.2-3) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../67-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby2.7. Preparing to unpack .../68-ruby2.7_2.7.4-1_armhf.deb ... Unpacking ruby2.7 (2.7.4-1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../69-ruby-rubygems_3.2.5-2_all.deb ... Unpacking ruby-rubygems (3.2.5-2) ... Selecting previously unselected package ruby. Preparing to unpack .../70-ruby_1%3a2.7+2_armhf.deb ... Unpacking ruby (1:2.7+2) ... Selecting previously unselected package rake. Preparing to unpack .../71-rake_13.0.3-1_all.deb ... Unpacking rake (13.0.3-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../72-ruby-minitest_5.13.0-1_all.deb ... Unpacking ruby-minitest (5.13.0-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../73-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../74-ruby-power-assert_1.1.7-2_all.deb ... Unpacking ruby-power-assert (1.1.7-2) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../75-ruby-test-unit_3.3.9-1_all.deb ... Unpacking ruby-test-unit (3.3.9-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../76-ruby-xmlrpc_0.3.0-2_all.deb ... Unpacking ruby-xmlrpc (0.3.0-2) ... Selecting previously unselected package libyaml-0-2:armhf. Preparing to unpack .../77-libyaml-0-2_0.2.2-1_armhf.deb ... Unpacking libyaml-0-2:armhf (0.2.2-1) ... Selecting previously unselected package libruby2.7:armhf. Preparing to unpack .../78-libruby2.7_2.7.4-1_armhf.deb ... Unpacking libruby2.7:armhf (2.7.4-1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../79-pkg-config_0.29.2-1_armhf.deb ... Unpacking pkg-config (0.29.2-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../80-python3-all_3.9.2-3_armhf.deb ... Unpacking python3-all (3.9.2-3) ... Selecting previously unselected package python3.9-dev. Preparing to unpack .../81-python3.9-dev_3.9.2-1_armhf.deb ... Unpacking python3.9-dev (3.9.2-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../82-python3-dev_3.9.2-3_armhf.deb ... Unpacking python3-dev (3.9.2-3) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../83-python3-all-dev_3.9.2-3_armhf.deb ... Unpacking python3-all-dev (3.9.2-3) ... Selecting previously unselected package samtools. Preparing to unpack .../84-samtools_1.11-1_armhf.deb ... Unpacking samtools (1.11-1) ... Selecting previously unselected package swig4.0. Preparing to unpack .../85-swig4.0_4.0.2-1_armhf.deb ... Unpacking swig4.0 (4.0.2-1) ... Selecting previously unselected package swig. Preparing to unpack .../86-swig_4.0.2-1_all.deb ... Unpacking swig (4.0.2-1) ... Selecting previously unselected package time. Preparing to unpack .../87-time_1.9-0.1_armhf.deb ... Unpacking time (1.9-0.1) ... Selecting previously unselected package yaggo. Preparing to unpack .../88-yaggo_1.5.10-2_all.deb ... Unpacking yaggo (1.5.10-2) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:armhf (1.5.3-1) ... Setting up time (1.9-0.1) ... Setting up libpsl5:armhf (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:armhf (67.1-7) ... Setting up ruby-power-assert (1.1.7-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:armhf (0.2.2-1) ... Setting up libglib2.0-0:armhf (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:armhf (1.0.9-2+b2) ... Setting up libnghttp2-14:armhf (1.43.0-1) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up libdeflate0:armhf (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2.1) ... Setting up ruby-minitest (5.13.0-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libexpat1-dev:armhf (2.2.10-2) ... Setting up ruby-test-unit (3.3.9-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:armhf (6.2+20201114-2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:armhf (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up d-shlibs (0.98) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2.1) ... Setting up liblzma-dev:armhf (5.2.5-2) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Setting up libmd0:armhf (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libmpdec3:armhf (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:armhf (1.9.0-2) ... Setting up dos2unix (7.4.1-1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up swig4.0 (4.0.2-1) ... Setting up openssl (1.1.1k-1) ... Setting up libbsd0:armhf (0.11.3-1) ... Setting up libdeflate-dev:armhf (1.7-1) ... Setting up libelf1:armhf (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7) ... Setting up chrpath (0.16-2+b1) ... Setting up libprocps8:armhf (2:3.3.17-5) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up swig (4.0.2-1) ... Setting up libtool (2.4.6-15) ... Setting up libedit2:armhf (3.1-20191231-2+b1) ... Setting up libreadline8:armhf (8.1-1) ... Setting up bc (1.07.1-2+b2) ... Setting up libldap-2.4-2:armhf (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:armhf (7.74.0-1.3+b1) ... Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libpython3.9-stdlib:armhf (3.9.2-1) ... Setting up libpython3-stdlib:armhf (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:armhf (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:armhf (1.11-4) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.11-1) ... Setting up dh-autoreconf (20) ... Setting up libpython3.9:armhf (3.9.2-1) ... Setting up python3.9 (3.9.2-1) ... Setting up libpython3.9-dev:armhf (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up python3.9-dev (3.9.2-1) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up libpython3-dev:armhf (3.9.2-3) ... Setting up python3-all (3.9.2-3) ... Setting up libpython3-all-dev:armhf (3.9.2-3) ... Setting up python3-dev (3.9.2-3) ... Setting up python3-all-dev (3.9.2-3) ... Setting up ruby2.7 (2.7.4-1) ... Setting up ruby-rubygems (3.2.5-2) ... Setting up ruby (1:2.7+2) ... Setting up rake (13.0.3-1) ... Setting up yaggo (1.5.10-2) ... Setting up libruby2.7:armhf (2.7.4-1) ... Processing triggers for libc-bin (2.31-13) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (432 kB/s) Selecting previously unselected package libnumber-compare-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 26233 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package hostname: Name or service not known I: Running cd /build/jellyfish-2.3.0/ && 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 > ../jellyfish_2.3.0-10_source.changes dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.3.0-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --with python3 debian/rules override_dh_clean make[1]: Entering directory '/build/jellyfish-2.3.0' dh_clean if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi rm -f tests/compat.sh rm -f swig/python/jellyfish* # swig/python/dna_jellyfish.py rm -f swig/perl5/blib/arch/auto/jellyfish/jellyfish.so rm -f swig/perl5/blib/bin/.exists rm -f swig/perl5/blib/lib/.exists rm -f swig/perl5/blib/lib/auto/jellyfish/.exists rm -f swig/perl5/blib/man1/.exists rm -f swig/perl5/blib/man3/.exists rm -f swig/perl5/blib/script/.exists rm -f swig/perl5/jellyfish.bs rm -f swig/perl5/pm_to_blib rm -rf swig/perl5/MYMETA.json swig/perl5/MYMETA.yml swig/perl5/Makefile swig/perl5/blib/ make[1]: Leaving directory '/build/jellyfish-2.3.0' debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:8: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/jellyfish-2.3.0' dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking 32-bit host C ABI... yes checking for ELF binary format... yes checking for the common suffixes of directories in the library search path... lib,lib,lib checking for htslib... yes checking for samtools... /usr/bin/samtools checking for unix2dos... /usr/bin/unix2dos checking for md5sum... md5sum checking for yaggo... /usr/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for __int128... no checking for std::numeric_limits<__int128>... no checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for sys/syscall.h... yes checking for siginfo_t.si_int... yes checking for swig... /usr/bin/swig checking SWIG version... 4.0.2 checking for SWIG library... /usr/share/swig4.0 checking for python... /usr/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python3.9 checking for Python library path... -L/usr/lib -lpython3.9 checking for Python site-packages path... /usr/lib/python3/dist-packages checking python extra libraries... -lcrypt -lpthread -ldl -lutil -lm -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes checking for perl... /usr/bin/perl checking for Perl prefix... /usr checking for Perl extension include path... /usr/lib/arm-linux-gnueabihf/perl/5.32/CORE checking for Perl extension target directory... /usr/lib/perl/5.32.0 checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_configure --sourcedirectory=swig/perl5 cd swig/perl5 && perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread" -I/build/jellyfish-2.3.0/debian/tmp//usr/include/jellyfish-2.3.0 -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -lpthread -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf Warning (mostly harmless): No library found for -ljellyfish-2.0 Generating a Unix-style Makefile Writing Makefile for jellyfish Writing MYMETA.yml and MYMETA.json dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config running config make[1]: Leaving directory '/build/jellyfish-2.3.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/jellyfish-2.3.0' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all bin/fastq2sam make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam make[2]: Entering directory '/build/jellyfish-2.3.0' /usr/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo /usr/bin/swig -c++ -python -I./../include -o swig/python/swig_wrap.cpp swig/jellyfish.i /usr/bin/swig -c++ -perl5 -I./../include -o swig/perl5/swig_wrap.cpp swig/jellyfish.i make all-am make[3]: Entering directory '/build/jellyfish-2.3.0' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/count_main.o sub_commands/count_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/info_main.o sub_commands/info_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/dump_main.o sub_commands/dump_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/histo_main.o sub_commands/histo_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/stats_main.o sub_commands/stats_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/merge_main.o sub_commands/merge_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/bc_main.o sub_commands/bc_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/query_main.o sub_commands/query_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/cite_main.o sub_commands/cite_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/mem_main.o sub_commands/mem_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/merge_files.o jellyfish/merge_files.cc /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o lib/rectangular_binary_matrix.lo lib/rectangular_binary_matrix.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/rectangular_binary_matrix.cc -fPIC -DPIC -o lib/.libs/rectangular_binary_matrix.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/rectangular_binary_matrix.cc -o lib/rectangular_binary_matrix.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o lib/mer_dna.lo lib/mer_dna.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/mer_dna.cc -fPIC -DPIC -o lib/.libs/mer_dna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/mer_dna.cc -o lib/mer_dna.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o lib/storage.lo lib/storage.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/storage.cc -fPIC -DPIC -o lib/.libs/storage.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/storage.cc -o lib/storage.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o lib/allocators_mmap.lo lib/allocators_mmap.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/allocators_mmap.cc -fPIC -DPIC -o lib/.libs/allocators_mmap.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/allocators_mmap.cc -o lib/allocators_mmap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o lib/misc.lo lib/misc.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/misc.cc -fPIC -DPIC -o lib/.libs/misc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/misc.cc -o lib/misc.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o lib/int128.lo lib/int128.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/int128.cc -fPIC -DPIC -o lib/.libs/int128.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/int128.cc -o lib/int128.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o lib/thread_exec.lo lib/thread_exec.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/thread_exec.cc -fPIC -DPIC -o lib/.libs/thread_exec.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/thread_exec.cc -o lib/thread_exec.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o lib/jsoncpp.lo lib/jsoncpp.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/jsoncpp.cpp -fPIC -DPIC -o lib/.libs/jsoncpp.o In file included from /usr/include/c++/10/map:60, from ./include/jellyfish/json.h:331, from lib/jsoncpp.cpp:76: /usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {std::pair&}; _Key = Json::Value::CZString; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from ./include/jellyfish/json.h:331, from lib/jsoncpp.cpp:76: /usr/include/c++/10/bits/stl_map.h: In member function 'Json::Value& Json::Value::operator[](Json::Value::ArrayIndex)': /usr/include/c++/10/bits/stl_map.h:877:38: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 877 | return _M_t._M_emplace_hint_unique(__position, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 878 | std::forward<_Pair>(__x)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In member function 'Json::Value& Json::Value::resolveReference(const char*, bool)': /usr/include/c++/10/bits/stl_map.h:877:38: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 877 | return _M_t._M_emplace_hint_unique(__position, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 878 | std::forward<_Pair>(__x)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/jsoncpp.cpp -o lib/jsoncpp.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o lib/time.lo lib/time.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/time.cc -fPIC -DPIC -o lib/.libs/time.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/time.cc -o lib/time.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o lib/generator_manager.lo lib/generator_manager.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/generator_manager.cc -fPIC -DPIC -o lib/.libs/generator_manager.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c lib/generator_manager.cc -o lib/generator_manager.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -version-info 2:0:0 -Wl,-z,relro -Wl,-z,now -lpthread -o libjellyfish-2.0.la -rpath /usr/lib/arm-linux-gnueabihf lib/rectangular_binary_matrix.lo lib/mer_dna.lo lib/storage.lo lib/allocators_mmap.lo lib/misc.lo lib/int128.lo lib/thread_exec.lo lib/jsoncpp.lo lib/time.lo lib/generator_manager.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o lib/.libs/rectangular_binary_matrix.o lib/.libs/mer_dna.o lib/.libs/storage.o lib/.libs/allocators_mmap.o lib/.libs/misc.o lib/.libs/int128.o lib/.libs/thread_exec.o lib/.libs/jsoncpp.o lib/.libs/time.o lib/.libs/generator_manager.o -lpthread -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libjellyfish-2.0.so.2 -o .libs/libjellyfish-2.0.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libjellyfish-2.0.so.2" && ln -s "libjellyfish-2.0.so.2.0.0" "libjellyfish-2.0.so.2") libtool: link: (cd ".libs" && rm -f "libjellyfish-2.0.so" && ln -s "libjellyfish-2.0.so.2.0.0" "libjellyfish-2.0.so") libtool: link: ar cr .libs/libjellyfish-2.0.a lib/rectangular_binary_matrix.o lib/mer_dna.o lib/storage.o lib/allocators_mmap.o lib/misc.o lib/int128.o lib/thread_exec.o lib/jsoncpp.o lib/time.o lib/generator_manager.o libtool: link: ranlib .libs/libjellyfish-2.0.a libtool: link: ( cd ".libs" && rm -f "libjellyfish-2.0.la" && ln -s "../libjellyfish-2.0.la" "libjellyfish-2.0.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -R/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -lpthread -o bin/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o libjellyfish-2.0.la libtool: link: g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/arm-linux-gnueabihf/perl/5.32/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -Wno-error -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo `test -f 'swig/perl5/swig_wrap.cpp' || echo './'`swig/perl5/swig_wrap.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/arm-linux-gnueabihf/perl/5.32/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -Wno-error -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c swig/perl5/swig_wrap.cpp -fPIC -DPIC -o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -I/usr/lib/arm-linux-gnueabihf/perl/5.32/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -Wno-error -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c swig/perl5/swig_wrap.cpp -o swig/perl5/swig_perl5_jellyfish_la-swig_wrap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -Wno-error -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.32.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -Wl,-rpath -Wl,/build/jellyfish-2.3.0/.libs -lpthread ./.libs/libjellyfish-2.0.so -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: link: (cd "swig/perl5/.libs" && rm -f "jellyfish.so.0" && ln -s "jellyfish.so.0.0.0" "jellyfish.so.0") libtool: link: (cd "swig/perl5/.libs" && rm -f "jellyfish.so" && ln -s "jellyfish.so.0.0.0" "jellyfish.so") libtool: link: ar cr swig/perl5/.libs/jellyfish.a swig/perl5/swig_perl5_jellyfish_la-swig_wrap.o libtool: link: ranlib swig/perl5/.libs/jellyfish.a libtool: link: ( cd "swig/perl5/.libs" && rm -f "jellyfish.la" && ln -s "../jellyfish.la" "jellyfish.la" ) /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.9 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo `test -f 'swig/python/swig_wrap.cpp' || echo './'`swig/python/swig_wrap.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.9 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c swig/python/swig_wrap.cpp -fPIC -DPIC -o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I/usr/include/python3.9 -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c swig/python/swig_wrap.cpp -o swig/python/swig_python__dna_jellyfish_la-swig_wrap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3/dist-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -Wl,-rpath -Wl,/build/jellyfish-2.3.0/.libs -lpthread ./.libs/libjellyfish-2.0.so -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: link: (cd "swig/python/.libs" && rm -f "_dna_jellyfish.so.0" && ln -s "_dna_jellyfish.so.0.0.0" "_dna_jellyfish.so.0") libtool: link: (cd "swig/python/.libs" && rm -f "_dna_jellyfish.so" && ln -s "_dna_jellyfish.so.0.0.0" "_dna_jellyfish.so") libtool: link: ar cr swig/python/.libs/_dna_jellyfish.a swig/python/swig_python__dna_jellyfish_la-swig_wrap.o libtool: link: ranlib swig/python/.libs/_dna_jellyfish.a libtool: link: ( cd "swig/python/.libs" && rm -f "_dna_jellyfish.la" && ln -s "../_dna_jellyfish.la" "_dna_jellyfish.la" ) /usr/bin/python3 -c 'import py_compile, sys; py_compile.compile(sys.argv[1], sys.argv[2])' swig/python/dna_jellyfish.py swig/python/__init__.pyc make[3]: Leaving directory '/build/jellyfish-2.3.0' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/generate_sequence.o jellyfish/generate_sequence.cc In file included from /usr/include/c++/10/vector:72, from jellyfish/generate_sequence.cc:10: /usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function 'void generate_sequence_args::parse(int, char**)': /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/backtrace.o jellyfish/backtrace.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/dbg.o jellyfish/dbg.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -R/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -lpthread -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o libjellyfish-2.0.la libtool: link: g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_main.o `test -f 'unit_tests/test_main.cc' || echo './'`unit_tests/test_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_misc.o `test -f 'unit_tests/test_misc.cc' || echo './'`unit_tests/test_misc.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_offsets_key_value.o `test -f 'unit_tests/test_offsets_key_value.cc' || echo './'`unit_tests/test_offsets_key_value.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_simple_circular_buffer.o `test -f 'unit_tests/test_simple_circular_buffer.cc' || echo './'`unit_tests/test_simple_circular_buffer.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_rectangular_binary_matrix.o `test -f 'unit_tests/test_rectangular_binary_matrix.cc' || echo './'`unit_tests/test_rectangular_binary_matrix.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_dna.o `test -f 'unit_tests/test_mer_dna.cc' || echo './'`unit_tests/test_mer_dna.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_large_hash_array.o `test -f 'unit_tests/test_large_hash_array.cc' || echo './'`unit_tests/test_large_hash_array.cc In file included from /usr/include/c++/10/map:60, from unit_tests/test_large_hash_array.cc:5: /usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple&>, std::tuple<>}; _Key = jellyfish::mer_dna_ns::mer_base_static; _Val = std::pair, long long unsigned int>; _KeyOfValue = std::_Select1st, long long unsigned int> >; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]': /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from unit_tests/test_large_hash_array.cc:5: /usr/include/c++/10/bits/stl_map.h: In function '{anonymous}::arrays_ptr {anonymous}::fill_array(size_t, size_t, int, int, int)': /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In member function 'virtual void {anonymous}::HashArray_Collisions_Test::TestBody()': /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In member function 'virtual void {anonymous}::Hash_Update_Test::TestBody()': /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o `test -f 'unit_tests/test_mer_overlap_sequence_parser.cc' || echo './'`unit_tests/test_mer_overlap_sequence_parser.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_file_header.o `test -f 'unit_tests/test_file_header.cc' || echo './'`unit_tests/test_file_header.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_iterator.o `test -f 'unit_tests/test_mer_iterator.cc' || echo './'`unit_tests/test_mer_iterator.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_hash_counter.o `test -f 'unit_tests/test_hash_counter.cc' || echo './'`unit_tests/test_hash_counter.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_heap.o `test -f 'unit_tests/test_mer_heap.cc' || echo './'`unit_tests/test_mer_heap.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_stream_iterator.o `test -f 'unit_tests/test_stream_iterator.cc' || echo './'`unit_tests/test_stream_iterator.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_token_ring.o `test -f 'unit_tests/test_token_ring.cc' || echo './'`unit_tests/test_token_ring.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_text_dumper.o `test -f 'unit_tests/test_text_dumper.cc' || echo './'`unit_tests/test_text_dumper.cc In file included from /usr/include/c++/10/map:60, from unit_tests/test_text_dumper.cc:1: /usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple&>, std::tuple<>}; _Key = jellyfish::mer_dna_ns::mer_base_static; _Val = std::pair, long long unsigned int>; _KeyOfValue = std::_Select1st, long long unsigned int> >; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]': /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/map:61, from unit_tests/test_text_dumper.cc:1: /usr/include/c++/10/bits/stl_map.h: In member function 'virtual void {anonymous}::hash_adder::start(int)': /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_map.h: In member function 'virtual void {anonymous}::TextDumper_Random_Test::TestBody()': /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_dumpers.o `test -f 'unit_tests/test_dumpers.cc' || echo './'`unit_tests/test_dumpers.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mapped_file.o `test -f 'unit_tests/test_mapped_file.cc' || echo './'`unit_tests/test_mapped_file.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_int128.o `test -f 'unit_tests/test_int128.cc' || echo './'`unit_tests/test_int128.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o `test -f 'unit_tests/test_mer_dna_bloom_counter.cc' || echo './'`unit_tests/test_mer_dna_bloom_counter.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_whole_sequence_parser.o `test -f 'unit_tests/test_whole_sequence_parser.cc' || echo './'`unit_tests/test_whole_sequence_parser.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_allocators_mmap.o `test -f 'unit_tests/test_allocators_mmap.cc' || echo './'`unit_tests/test_allocators_mmap.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_cooperative_pool2.o `test -f 'unit_tests/test_cooperative_pool2.cc' || echo './'`unit_tests/test_cooperative_pool2.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_generator_manager.o `test -f 'unit_tests/test_generator_manager.cc' || echo './'`unit_tests/test_generator_manager.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_atomic_bits_array.o `test -f 'unit_tests/test_atomic_bits_array.cc' || echo './'`unit_tests/test_atomic_bits_array.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_stdio_filebuf.o `test -f 'unit_tests/test_stdio_filebuf.cc' || echo './'`unit_tests/test_stdio_filebuf.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/bin_test_all-backtrace.o `test -f 'jellyfish/backtrace.cc' || echo './'`jellyfish/backtrace.cc /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/gtest/src/libgtest_la-gtest-all.lo `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c unit_tests/gtest/src/gtest-all.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c unit_tests/gtest/src/gtest-all.cc -o unit_tests/gtest/src/libgtest_la-gtest-all.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -R/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest.la unit_tests/gtest/src/libgtest_la-gtest-all.lo libtool: link: ar cr .libs/libgtest.a unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: link: ranlib .libs/libgtest.a libtool: link: ( cd ".libs" && rm -f "libgtest.la" && ln -s "../libgtest.la" "libgtest.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -R/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -lpthread -o bin/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o libgtest.la libjellyfish-2.0.la libtool: link: g++ -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf ./.libs/libgtest.a -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/fastq2sam.o jellyfish/fastq2sam.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -R/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -Wl,-z,relro -Wl,-z,now -lpthread -o bin/fastq2sam jellyfish/fastq2sam.o libjellyfish-2.0.la libtool: link: g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/fastq2sam jellyfish/fastq2sam.o -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf make[2]: Leaving directory '/build/jellyfish-2.3.0' dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-2.3.0' make install-am make[3]: Entering directory '/build/jellyfish-2.3.0' make[4]: Entering directory '/build/jellyfish-2.3.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-2.3.0/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/jellyfish-2.3.0/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/sh "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -Werror -Wno-error -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.32.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.32.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/sh "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3/dist-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-2.3.0' make[3]: Leaving directory '/build/jellyfish-2.3.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/sh "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -Werror -Wno-error -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.32.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.32.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/sh "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3/dist-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-2.3.0' dh_auto_build --sourcedirectory=swig/perl5 cd swig/perl5 && make -j4 make[2]: Entering directory '/build/jellyfish-2.3.0/swig/perl5' Running Mkbootstrap for jellyfish () g++ -c -std=c++0x -I/build/jellyfish-2.3.0/debian/tmp//usr/include/jellyfish-2.3.0 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.0.1\" -DXS_VERSION=\"0.0.1\" -fPIC "-I/usr/lib/arm-linux-gnueabihf/perl/5.32/CORE" swig_wrap.cpp chmod 644 "jellyfish.bs" "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 rm -f blib/arch/auto/jellyfish/jellyfish.so arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread -shared -L/usr/local/lib -fstack-protector-strong swig_wrap.o -o blib/arch/auto/jellyfish/jellyfish.so \ -lpthread \ chmod 755 blib/arch/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/jellyfish-2.3.0/swig/perl5' dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build build_ext -L/build/jellyfish-2.3.0/.libs running build running build_py copying dna_jellyfish.py -> /build/jellyfish-2.3.0/.pybuild/cpython3_3.9_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build creating build/temp.linux-armhf-3.9 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/jellyfish-2.3.0/debian/tmp//usr/include/jellyfish-2.3.0 -I/usr/include/python3.9 -c swig_wrap.cpp -o build/temp.linux-armhf-3.9/swig_wrap.o -std=c++0x arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/swig_wrap.o -L/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf -L/build/jellyfish-2.3.0/.libs -ljellyfish-2.0 -lpthread -o /build/jellyfish-2.3.0/.pybuild/cpython3_3.9_dna_jellyfish/build/_dna_jellyfish.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,/build/jellyfish-2.3.0/debian/tmp//usr/lib/arm-linux-gnueabihf make[1]: Leaving directory '/build/jellyfish-2.3.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/jellyfish-2.3.0' echo "Test data are to big for 32bit architectures thus no testing is done" Test data are to big for 32bit architectures thus no testing is done make[1]: Leaving directory '/build/jellyfish-2.3.0' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/jellyfish-2.3.0' chrpath --delete bin/.libs/* dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-2.3.0' make install-am make[3]: Entering directory '/build/jellyfish-2.3.0' make[4]: Entering directory '/build/jellyfish-2.3.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-2.3.0/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/jellyfish-2.3.0/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/sh "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -Werror -Wno-error -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.32.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.32.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/sh "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3/dist-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-2.3.0' make[3]: Leaving directory '/build/jellyfish-2.3.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/sh "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -Werror -Wno-error -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.32.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.32.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.32.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/sh "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3/dist-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-2.3.0' dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/jellyfish-2.3.0/debian/python3-dna-jellyfish running install running build running build_py running build_ext running install_lib creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.9 creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages copying /build/jellyfish-2.3.0/.pybuild/cpython3_3.9_dna_jellyfish/build/dna_jellyfish.py -> /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages copying /build/jellyfish-2.3.0/.pybuild/cpython3_3.9_dna_jellyfish/build/_dna_jellyfish.cpython-39-arm-linux-gnueabihf.so -> /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages byte-compiling /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-39.pyc running install_egg_info Writing /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages/dna_jellyfish-0.0.1.egg-info dh_auto_install --sourcedirectory=swig/perl5 cd swig/perl5 && make -j4 install DESTDIR=/build/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/build/jellyfish-2.3.0/swig/perl5' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/perl5/5.32/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/jellyfish-2.3.0/swig/perl5' ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so -r-xr-xr-x 1 pbuilder2 pbuilder2 1110424 Aug 13 01:48 debian/tmp/usr/lib/arm-linux-gnueabihf/perl5/5.32/auto/jellyfish/jellyfish.so if [ ! -e debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so ] ; then sleep 1; fi chmod +w debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp" usr/include/jellyfish \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.h" usr/include/jellyfish \ --movedev config.h usr/include/jellyfish \ debian/tmp/usr/lib/*/libjellyfish-*.so Library package automatic movement utility set -e install -d -m 755 debian/libjellyfish-2.0-dev/usr/lib/arm-linux-gnueabihf install -d -m 755 debian/libjellyfish-2.0-2/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a debian/libjellyfish-2.0-dev/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.la debian/libjellyfish-2.0-dev/usr/lib/arm-linux-gnueabihf || true mv debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so debian/libjellyfish-2.0-dev/usr/lib/arm-linux-gnueabihf mv /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2 debian/libjellyfish-2.0-2/usr/lib/arm-linux-gnueabihf mv /build/jellyfish-2.3.0/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2.0.0 debian/libjellyfish-2.0-2/usr/lib/arm-linux-gnueabihf PKGDEV=libjellyfish-2.0-dev PKGSHL=libjellyfish-2.0-2 install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.h debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv config.h debian/libjellyfish-2.0-dev/usr/include/jellyfish sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/arm-linux-gnueabihf/*.la chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so make[1]: Leaving directory '/build/jellyfish-2.3.0' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/jellyfish-2.3.0' # Python files are just installed rm -rf debian/tmp/usr/lib/python3/dist-packages # Necessary Perl files are just installed rm -rf debian/tmp/usr/lib/perl/5.32.0 dh_missing make[1]: Leaving directory '/build/jellyfish-2.3.0' dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/jellyfish/usr/lib/jellyfish/bin/test_all contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/jellyfish/usr/lib/jellyfish/bin/fastq2sam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/jellyfish/usr/lib/jellyfish/bin/generate_sequence contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/jellyfish/usr/bin/jellyfish contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libjellyfish-2.0-2/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2.0.0 found in none of the libraries dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package python3-dna-jellyfish: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-dna-jellyfish: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: Depends field of package jellyfish-examples: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-dna-jellyfish: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-dna-jellyfish: substitution variable ${python3:Versions} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.0-10_armhf.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.0-10_armhf.deb'. dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.0-10_armhf.deb'. dpkg-deb: building package 'jellyfish-examples' in '../jellyfish-examples_2.3.0-10_all.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.0-10_armhf.deb'. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.0-10_armhf.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.0-10_armhf.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.0-10_armhf.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.0-10_armhf.deb'. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.0-10_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../jellyfish_2.3.0-10_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . 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/14891/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/14891/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/14891 and its subdirectories I: Current time: Fri Aug 13 01:49:26 +14 2021 I: pbuilder-time-stamp: 1628768966