jellyfish →
2.3.0-12+b1 →
armhf → 2022-02-13 03:30:16
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| jellyfish 2.3.0-12+b1 (armhf) Sun, 13 Feb 2022 03:09:40 +0000 |
+==============================================================================+
Package: jellyfish
Version: 2.3.0-12+b1
Source Version: 2.3.0-12
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-4aa09996-641d-45f8-a82d-aec11bd3b0ab' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/jellyfish-EBKiTA/resolver-wcMNs3' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [12.8 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.6 MB]
Fetched 26.4 MB in 10s (2712 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'jellyfish' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/jellyfish.git
Please use:
git clone https://salsa.debian.org/med-team/jellyfish.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 697 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main jellyfish 2.3.0-12 (dsc) [3206 B]
Get:2 http://172.17.4.1/private bookworm-staging/main jellyfish 2.3.0-12 (tar) [679 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main jellyfish 2.3.0-12 (diff) [14.7 kB]
Fetched 697 kB in 0s (3405 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/jellyfish-EBKiTA/jellyfish-2.3.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/jellyfish-EBKiTA' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), d-shlibs, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), d-shlibs, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [446 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [527 B]
Fetched 1930 B in 0s (49.6 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bc bsdextrautils ca-certificates
chrpath d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism
dos2unix dwz file gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libbrotli1 libbsd0 libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libedit2 libelf1 libexpat1
libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev
libhts3 libhtscodecs2 libicu67 libjs-jquery libjs-sphinxdoc libjs-underscore
liblzma-dev libmagic-mgc libmagic1 libmd0 libmpdec3 libncurses6
libnghttp2-14 libpipeline1 libprocps8 libpsl5 libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.9 libpython3.9-dev
libpython3.9-minimal libpython3.9-stdlib librtmp1 libruby2.7 libsigsegv2
libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4
man-db media-types openssl pkg-config po-debconf procps python3 python3-all
python3-all-dev python3-dev python3-distutils python3-lib2to3
python3-minimal python3.9 python3.9-dev python3.9-minimal rake ruby
ruby-minitest ruby-net-telnet ruby-power-assert ruby-rubygems ruby-test-unit
ruby-xmlrpc ruby2.7 rubygems-integration samtools swig swig4.0 time yaggo
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build
python3-tomli python3-installer gettext-doc libasprintf-dev libgettextpo-dev
groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev liblzma-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv
python3.9-doc binfmt-support ri ruby-dev bundler cwltool swig-doc
swig-examples swig4.0-examples swig4.0-doc
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs javascript-common libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl psmisc zip fonts-lato
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bc bsdextrautils ca-certificates
chrpath d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism
dos2unix dwz file gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libbrotli1 libbsd0 libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libedit2 libelf1 libexpat1
libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev
libhts3 libhtscodecs2 libicu67 libjs-jquery libjs-sphinxdoc libjs-underscore
liblzma-dev libmagic-mgc libmagic1 libmd0 libmpdec3 libncurses6
libnghttp2-14 libpipeline1 libprocps8 libpsl5 libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.9 libpython3.9-dev
libpython3.9-minimal libpython3.9-stdlib librtmp1 libruby2.7 libsigsegv2
libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4
man-db media-types openssl pkg-config po-debconf procps python3 python3-all
python3-all-dev python3-dev python3-distutils python3-lib2to3
python3-minimal python3.9 python3.9-dev python3.9-minimal rake ruby
ruby-minitest ruby-net-telnet ruby-power-assert ruby-rubygems ruby-test-unit
ruby-xmlrpc ruby2.7 rubygems-integration samtools
sbuild-build-depends-main-dummy swig swig4.0 time yaggo zlib1g-dev
0 upgraded, 101 newly installed, 0 to remove and 19 not upgraded.
Need to get 45.6 MB of archives.
After this operation, 155 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [952 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.10-1+rpi1 [794 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.4-1 [82.4 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.10-1+rpi1 [1595 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.7-1+b4 [38.7 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf media-types all 5.0.0 [32.5 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.10-1+rpi1 [1611 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf python3.9 armhf 3.9.10-1+rpi1 [488 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.7-1+b4 [21.8 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.9.7-1+b4 [38.3 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.3-1 [136 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.5-1 [32.9 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.0-2 [1356 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3-2 [79.6 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-6 [60.6 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-6 [476 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf bc armhf 1.07.1-3 [101 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 1.1.1m-1 [815 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20211016 [156 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf time armhf 1.9-0.1 [50.5 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf d-shlibs all 0.104 [18.6 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.6 [193 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.6 [1054 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.10-1 [79.4 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.9.10-1 [146 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220119 [110 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf dos2unix armhf 7.4.2-2 [391 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.5-1 [108 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.81.0-1 [315 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.81.0-1 [391 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.8-1 [40.4 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.4.4-1 [135 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.3-1 [1209 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-3 [49.8 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libhts-dev armhf 1.13+ds-2 [4049 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-8 [315 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libjs-underscore all 1.13.2~dfsg-2 [116 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libjs-sphinxdoc all 4.3.2-1 [139 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9 armhf 3.9.10-1+rpi1 [1419 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-dev armhf 3.9.10-1+rpi1 [3015 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libpython3-dev armhf 3.9.7-1+b4 [22.1 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libpython3-all-dev armhf 3.9.7-1+b4 [1068 B]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf rubygems-integration all 1.18 [6704 B]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf ruby2.7 armhf 2.7.4-1+b1 [747 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf ruby-rubygems all 3.3.5-2 [289 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf ruby armhf 1:2.7.6 [11.9 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf rake all 13.0.6-2 [83.9 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf ruby-minitest all 5.13.0-2 [57.3 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf ruby-power-assert all 1.1.7-2 [11.5 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf ruby-test-unit all 3.3.9-1 [86.1 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf ruby-xmlrpc all 0.3.2-1 [24.3 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libyaml-0-2 armhf 0.2.2-1 [40.0 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libruby2.7 armhf 2.7.4-1+b1 [3902 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf python3-all armhf 3.9.7-1+b4 [1060 B]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf python3.9-dev armhf 3.9.10-1+rpi1 [501 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf python3-dev armhf 3.9.7-1+b4 [25.3 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf python3-all-dev armhf 3.9.7-1+b4 [1076 B]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf samtools armhf 1.13-4 [525 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf swig4.0 armhf 4.0.2-2 [1221 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf swig all 4.0.2-2 [330 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf yaggo all 1.5.10-5 [21.4 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libhtscodecs2:armhf (1.1.1-3) ...
Setting up media-types (5.0.0) ...
Setting up libpipeline1:armhf (1.5.5-1) ...
Setting up time (1.9-0.1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.3-1) ...
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No schema files found: doing nothing.
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Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.41-2) ...
Setting up libdeflate0:armhf (1.8-1) ...
Setting up bc (1.07.1-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.41-2) ...
Setting up ruby-minitest (5.13.0-2) ...
Setting up autotools-dev (20220109.1) ...
Setting up libexpat1-dev:armhf (2.4.4-1) ...
Setting up ruby-test-unit (3.3.9-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.3-2) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up libsigsegv2:armhf (2.14-1) ...
Setting up autopoint (0.21-4) ...
Setting up pkg-config (0.29.2-1) ...
Setting up d-shlibs (0.104) ...
Setting up liblzma-dev:armhf (5.2.5-2) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libmd0:armhf (1.0.4-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.10.0-2) ...
Setting up dos2unix (7.4.2-2) ...
Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-8) ...
Setting up swig4.0 (4.0.2-2) ...
Setting up openssl (1.1.1m-1) ...
Setting up libbsd0:armhf (0.11.5-1) ...
Setting up libdeflate-dev:armhf (1.8-1) ...
Setting up libelf1:armhf (0.186-1) ...
Setting up ruby-xmlrpc (0.3.2-1) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up chrpath (0.16-2) ...
Setting up libprocps8:armhf (2:3.3.17-6) ...
Setting up libpython3.9-stdlib:armhf (3.9.10-1+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.7-1+b4) ...
Setting up libjs-underscore (1.13.2~dfsg-2) ...
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up gettext (0.21-4) ...
Setting up swig (4.0.2-2) ...
Setting up libtool (2.4.6-15) ...
Setting up libedit2:armhf (3.1-20210910-1) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.81.0-1) ...
Setting up libcurl4-gnutls-dev:armhf (7.81.0-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
127 added, 0 removed; done.
Setting up libpython3.9:armhf (3.9.10-1+rpi1) ...
Setting up libjs-sphinxdoc (4.3.2-1) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-8) ...
Setting up procps (2:3.3.17-6) ...
Setting up python3.9 (3.9.10-1+rpi1) ...
Setting up automake (1:1.16.5-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.13+ds-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.13+ds-2) ...
Setting up libpython3.9-dev:armhf (3.9.10-1+rpi1) ...
Setting up python3 (3.9.7-1+b4) ...
Setting up rubygems-integration (1.18) ...
Setting up man-db (2.10.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.13-4) ...
Setting up dh-autoreconf (20) ...
Setting up python3.9-dev (3.9.10-1+rpi1) ...
Setting up python3-lib2to3 (3.9.10-1) ...
Setting up python3-distutils (3.9.10-1) ...
Setting up dh-python (5.20220119) ...
Setting up libpython3-dev:armhf (3.9.7-1+b4) ...
Setting up python3-all (3.9.7-1+b4) ...
Setting up debhelper (13.6) ...
Setting up libpython3-all-dev:armhf (3.9.7-1+b4) ...
Setting up python3-dev (3.9.7-1+b4) ...
Setting up python3-all-dev (3.9.7-1+b4) ...
Setting up rake (13.0.6-2) ...
Setting up ruby-rubygems (3.3.5-2) ...
Setting up libruby2.7:armhf (2.7.4-1+b1) ...
Setting up ruby2.7 (2.7.4-1+b1) ...
Setting up ruby (1:2.7.6) ...
Setting up yaggo (1.5.10-5) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.33-5+rpi1) ...
Processing triggers for ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64 all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.37.90.20220130-2+rpi2 dpkg-dev_1.21.1+rpi1 g++-11_11.2.0-14+rpi1 gcc-11_11.2.0-14+rpi1 libc6-dev_2.33-5+rpi1 libstdc++-11-dev_11.2.0-14+rpi1 libstdc++6_11.2.0-14+rpi1 linux-libc-dev_5.14.16-1+rpi1
Package versions: adduser_3.118 apt_2.3.15 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20220109.1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-6 bc_1.07.1-3 binutils_2.37.90.20220130-2+rpi2 binutils-arm-linux-gnueabihf_2.37.90.20220130-2+rpi2 binutils-common_2.37.90.20220130-2+rpi2 bsdextrautils_2.37.3-1 bsdutils_1:2.37.3-1 build-essential_12.9 bzip2_1.0.8-5 ca-certificates_20211016 chrpath_0.16-2 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-14+rpi1 d-shlibs_0.104 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.6 debianutils_4.11.2 dh-autoreconf_20 dh-python_5.20220119 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-3 dos2unix_7.4.2-2 dpkg_1.21.1+rpi1 dpkg-dev_1.21.1+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.27-1 file_1:5.41-2 findutils_4.8.0-1 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-14+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-14+rpi1 gcc-11-base_11.2.0-14+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-3 gnupg-l10n_2.2.27-3 gnupg-utils_2.2.27-3 gpg_2.2.27-3 gpg-agent_2.2.27-3 gpg-wks-client_2.2.27-3 gpg-wks-server_2.2.27-3 gpgconf_2.2.27-3 gpgsm_2.2.27-3 gpgv_2.2.27-3 grep_3.7-1 groff-base_1.22.4-8 gzip_1.10-4 hostname_3.23 init-system-helpers_1.61 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.15 libarchive-zip-perl_1.68-1 libasan6_11.2.0-14+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-14+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37.90.20220130-2+rpi2 libblkid1_2.37.3-1 libbrotli1_1.0.9-2+b1 libbsd0_0.11.5-1 libbz2-1.0_1.0.8-5 libc-bin_2.33-5+rpi1 libc-dev-bin_2.33-5+rpi1 libc6_2.33-5+rpi1 libc6-dev_2.33-5+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-14+rpi1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.37.90.20220130-2+rpi2 libctf0_2.37.90.20220130-2+rpi2 libcurl3-gnutls_7.81.0-1 libcurl4-gnutls-dev_7.81.0-1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.6 libdeflate-dev_1.8-1 libdeflate0_1.8-1 libdpkg-perl_1.21.1+rpi1 libedit2_3.1-20210910-1 libelf1_0.186-1 libexpat1_2.4.4-1 libexpat1-dev_2.4.4-1 libext2fs2_1.46.5-2 libfakeroot_1.27-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.2.0-14+rpi1 libgcc-s1_11.2.0-14+rpi1 libgcrypt20_1.9.4-5 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libglib2.0-0_2.70.3-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.3-4 libgomp1_11.2.0-14+rpi1 libgpg-error0_1.43-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libjs-jquery_3.5.1+dfsg+~3.5.5-8 libjs-sphinxdoc_4.3.2-1 libjs-underscore_1.13.2~dfsg-2 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmd0_1.0.4-1 libmount1_2.37.3-1 libmpc3_1.2.1-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.3-2 libncursesw6_6.3-2 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libperl5.34_5.34.0-3 libpipeline1_1.5.5-1 libprocps8_2:3.3.17-6 libpsl5_0.21.0-1.2 libpython3-all-dev_3.9.7-1+b4 libpython3-dev_3.9.7-1+b4 libpython3-stdlib_3.9.7-1+b4 libpython3.9_3.9.10-1+rpi1 libpython3.9-dev_3.9.10-1+rpi1 libpython3.9-minimal_3.9.10-1+rpi1 libpython3.9-stdlib_3.9.10-1+rpi1 libreadline8_8.1.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libruby2.7_2.7.4-1+b1 libsasl2-2_2.1.27+dfsg2-3 libsasl2-modules-db_2.1.27+dfsg2-3 libseccomp2_2.5.3-2+rpi1 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.14-1 libsmartcols1_2.37.3-1 libsqlite3-0_3.37.2-2 libss2_1.46.5-2 libssh2-1_1.10.0-2 libssl1.1_1.1.1m-1 libstdc++-11-dev_11.2.0-14+rpi1 libstdc++6_11.2.0-14+rpi1 libsub-override-perl_0.09-2 libsystemd0_250.3-2+rpi1 libtasn1-6_4.18.0-4 libtinfo6_6.3-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-14+rpi1 libuchardet0_0.0.7-1 libudev1_250.3-2+rpi1 libunistring2_1.0-1 libuuid1_2.37.3-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libyaml-0-2_0.2.2-1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.16-1+rpi1 login_1:4.11.1+dfsg1-1 logsave_1.46.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.0-2 mawk_1.3.4.20200120-3 media-types_5.0.0 mount_2.37.3-1 ncurses-base_6.3-2 ncurses-bin_6.3-2 openssl_1.1.1m-1 passwd_1:4.11.1+dfsg1-1 patch_2.7.6-7 perl_5.34.0-3 perl-base_5.34.0-3 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-3 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 procps_2:3.3.17-6 python3_3.9.7-1+b4 python3-all_3.9.7-1+b4 python3-all-dev_3.9.7-1+b4 python3-dev_3.9.7-1+b4 python3-distutils_3.9.10-1 python3-lib2to3_3.9.10-1 python3-minimal_3.9.7-1+b4 python3.9_3.9.10-1+rpi1 python3.9-dev_3.9.10-1+rpi1 python3.9-minimal_3.9.10-1+rpi1 rake_13.0.6-2 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1 rpcsvc-proto_1.4.2-4 ruby_1:2.7.6 ruby-minitest_5.13.0-2 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-2 ruby-rubygems_3.3.5-2 ruby-test-unit_3.3.9-1 ruby-xmlrpc_0.3.2-1 ruby2.7_2.7.4-1+b1 rubygems-integration_1.18 samtools_1.13-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 swig_4.0.2-2 swig4.0_4.0.2-2 sysvinit-utils_3.01-1 tar_1.34+dfsg-1 time_1.9-0.1 tzdata_2021e-1 util-linux_2.37.3-1 xz-utils_5.2.5-2 yaggo_1.5.10-5 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: jellyfish
Binary: jellyfish, libjellyfish-2.0-2, libjellyfish-2.0-dev, python3-dna-jellyfish, libjellyfish-perl, jellyfish-examples
Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64 all
Version: 2.3.0-12
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Shaun Jackman <sjackman@debian.org>, Andreas Tille <tille@debian.org>, Michael R. Crusoe <crusoe@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://github.com/gmarcais/Jellyfish
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
Testsuite: autopkgtest
Testsuite-Triggers: @builddeps@
Build-Depends: debhelper-compat (= 13), d-shlibs, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools
Package-List:
jellyfish deb science optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64
jellyfish-examples deb science optional arch=all
libjellyfish-2.0-2 deb libs optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64
libjellyfish-2.0-dev deb libdevel optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64
libjellyfish-perl deb perl optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64
python3-dna-jellyfish deb python optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64
Checksums-Sha1:
4f7f5263e6e097c623531a660ef6158e2fb5e17b 679125 jellyfish_2.3.0.orig.tar.gz
4d2b3679caed78b6b252e68ce7dd6a033a7c2dd8 14748 jellyfish_2.3.0-12.debian.tar.xz
Checksums-Sha256:
29ead991de90151dbe4a2717f7ac30b3852296c9cbdda8b001121a1f2fa714db 679125 jellyfish_2.3.0.orig.tar.gz
7251f85e2b9617d4d05ebc1d56af08d62ff2c5489fce94a66e1160272e8b6076 14748 jellyfish_2.3.0-12.debian.tar.xz
Files:
b447a26df0f1e11526129907a9b0acdb 679125 jellyfish_2.3.0.orig.tar.gz
6890c95118c11bdb03e47b801d6d0de9 14748 jellyfish_2.3.0-12.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.6abcODMo/trustedkeys.kbx': General error
gpgv: Signature made Tue Aug 31 07:37:51 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./jellyfish_2.3.0-12.dsc
dpkg-source: info: extracting jellyfish in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking jellyfish_2.3.0.orig.tar.gz
dpkg-source: info: unpacking jellyfish_2.3.0-12.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
dpkg-source: info: applying fix-autoreconf.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.3.0-12+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=12b0d11b34b646c0abd5fc586dfab6e4
JOURNAL_STREAM=8:22125
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-4aa09996-641d-45f8-a82d-aec11bd3b0ab
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c23062
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package jellyfish
dpkg-buildpackage: info: source version 2.3.0-12+b1
dpkg-buildpackage: info: source distribution bookworm-staging
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 '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
debian/rules binary-arch
dh binary-arch --with python3
dh_update_autotools_config -a
dh_autoreconf -a
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: warning: The macro `AC_PROG_LIBTOOL' is obsolete.
configure.ac:8: You should run autoupdate.
m4/libtool.m4:99: AC_PROG_LIBTOOL is expanded from...
configure.ac:8: the top level
configure.ac:65: warning: The macro `AC_TRY_RUN' is obsolete.
configure.ac:65: You should run autoupdate.
./lib/autoconf/general.m4:2997: AC_TRY_RUN is expanded from...
lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
m4/m4-ax_ext.m4:49: AX_EXT is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
configure.ac:65: the top level
configure.ac:107: warning: The macro `AC_HELP_STRING' is obsolete.
configure.ac:107: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from...
configure.ac:107: the top level
configure.ac:118: warning: The macro `AC_HELP_STRING' is obsolete.
configure.ac:118: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from...
configure.ac:118: the top level
configure.ac:121: warning: The macro `AC_HELP_STRING' is obsolete.
configure.ac:121: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from...
configure.ac:121: the top level
configure.ac:124: warning: The macro `AC_HELP_STRING' is obsolete.
configure.ac:124: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from...
configure.ac:124: the top level
configure.ac:127: warning: The macro `AC_HELP_STRING' is obsolete.
configure.ac:127: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from...
configure.ac:127: the top level
configure.ac:131: warning: The macro `AC_HELP_STRING' is obsolete.
configure.ac:131: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from...
configure.ac:131: the top level
configure.ac:135: warning: The macro `SWIG_ENABLE_CXX' is obsolete.
configure.ac:135: You should run autoupdate.
m4/m4-ax_swig_enable_cxx.m4:48: SWIG_ENABLE_CXX is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
configure.ac:135: the top level
configure.ac:145: warning: The macro `AC_HELP_STRING' is obsolete.
configure.ac:145: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from...
configure.ac:145: the top level
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 '/<<PKGBUILDDIR>>'
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 race-free mkdir -p... /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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... 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... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /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... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.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 the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
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/arm-linux-gnueabihf -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/5.34/CORE
checking for Perl extension target directory... /usr/lib/perl/5.34.0
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 && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread"
-I/<<PKGBUILDDIR>>/debian/tmp//usr/include/jellyfish-2.3.0
-L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -lpthread
-L/<<PKGBUILDDIR>>/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:237: python3.9 setup.py config
running config
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
/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 '/<<PKGBUILDDIR>>'
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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++/11/map:60,
from ./include/jellyfish/json.h:331,
from lib/jsoncpp.cpp:76:
/usr/include/c++/11/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<const Json::Value::CZString, Json::Value>&}; _Key = Json::Value::CZString; _Val = std::pair<const Json::Value::CZString, Json::Value>; _KeyOfValue = std::_Select1st<std::pair<const Json::Value::CZString, Json::Value> >; _Compare = std::less<Json::Value::CZString>; _Alloc = std::allocator<std::pair<const Json::Value::CZString, Json::Value> >]’:
/usr/include/c++/11/bits/stl_tree.h:2428:7: note: parameter passing for argument of type ‘std::_Rb_tree<Json::Value::CZString, std::pair<const Json::Value::CZString, Json::Value>, std::_Select1st<std::pair<const Json::Value::CZString, Json::Value> >, std::less<Json::Value::CZString>, std::allocator<std::pair<const Json::Value::CZString, Json::Value> > >::const_iterator’ changed in GCC 7.1
2428 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from ./include/jellyfish/json.h:331,
from lib/jsoncpp.cpp:76:
/usr/include/c++/11/bits/stl_map.h: In member function ‘Json::Value& Json::Value::operator[](Json::Value::ArrayIndex)’:
/usr/include/c++/11/bits/stl_map.h:877:45: note: parameter passing for argument of type ‘std::map<Json::Value::CZString, Json::Value>::const_iterator’ {aka ‘std::_Rb_tree<Json::Value::CZString, std::pair<const Json::Value::CZString, Json::Value>, std::_Select1st<std::pair<const Json::Value::CZString, Json::Value> >, std::less<Json::Value::CZString>, std::allocator<std::pair<const Json::Value::CZString, Json::Value> > >::const_iterator’} changed in GCC 7.1
877 | return _M_t._M_emplace_hint_unique(__position,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
878 | std::forward<_Pair>(__x));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function ‘Json::Value& Json::Value::resolveReference(const char*, bool)’:
/usr/include/c++/11/bits/stl_map.h:877:45: note: parameter passing for argument of type ‘std::map<Json::Value::CZString, Json::Value>::const_iterator’ {aka ‘std::_Rb_tree<Json::Value::CZString, std::pair<const Json::Value::CZString, Json::Value>, std::_Select1st<std::pair<const Json::Value::CZString, Json::Value> >, std::less<Json::Value::CZString>, std::allocator<std::pair<const Json::Value::CZString, Json::Value> > >::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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/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/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/11/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -R/<<PKGBUILDDIR>>/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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf
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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/5.34/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/5.34/CORE -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
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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" )
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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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
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libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -Wl,-rpath -Wl,/<<PKGBUILDDIR>>/.libs -lpthread ./.libs/libjellyfish-2.0.so -L/usr/lib/gcc/arm-linux-gnueabihf/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/11/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../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")
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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 '/<<PKGBUILDDIR>>'
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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++/11/vector:72,
from jellyfish/generate_sequence.cc:10:
/usr/include/c++/11/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<long long unsigned int>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void generate_sequence_args::parse(int, char**)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ 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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/dbg.o jellyfish/dbg.cc
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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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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++/11/map:60,
from unit_tests/test_large_hash_array.cc:5:
/usr/include/c++/11/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<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>&>, std::tuple<>}; _Key = jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>; _Val = std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int>; _KeyOfValue = std::_Select1st<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >; _Compare = std::less<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0> >; _Alloc = std::allocator<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >]’:
/usr/include/c++/11/bits/stl_tree.h:2428:7: note: parameter passing for argument of type ‘std::_Rb_tree<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int>, std::_Select1st<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >, std::less<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0> >, std::allocator<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> > >::const_iterator’ changed in GCC 7.1
2428 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from unit_tests/test_large_hash_array.cc:5:
/usr/include/c++/11/bits/stl_map.h: In function ‘{anonymous}::arrays_ptr {anonymous}::fill_array(size_t, size_t, int, int, int)’:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int>, std::_Select1st<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >, std::less<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0> >, std::allocator<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, 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<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function ‘virtual void {anonymous}::HashArray_Collisions_Test::TestBody()’:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int>, std::_Select1st<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >, std::less<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0> >, std::allocator<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, 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<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int>, std::_Select1st<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >, std::less<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0> >, std::allocator<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, 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<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function ‘virtual void {anonymous}::Hash_Update_Test::TestBody()’:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int>, std::_Select1st<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >, std::less<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0> >, std::allocator<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, 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<const key_type&>(__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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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++/11/map:60,
from unit_tests/test_text_dumper.cc:1:
/usr/include/c++/11/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<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>&>, std::tuple<>}; _Key = jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>; _Val = std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int>; _KeyOfValue = std::_Select1st<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >; _Compare = std::less<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0> >; _Alloc = std::allocator<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >]’:
/usr/include/c++/11/bits/stl_tree.h:2428:7: note: parameter passing for argument of type ‘std::_Rb_tree<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int>, std::_Select1st<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >, std::less<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0> >, std::allocator<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> > >::const_iterator’ changed in GCC 7.1
2428 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from unit_tests/test_text_dumper.cc:1:
/usr/include/c++/11/bits/stl_map.h: In member function ‘virtual void {anonymous}::hash_adder::start(int)’:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int>, std::_Select1st<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >, std::less<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0> >, std::allocator<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, 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<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function ‘virtual void {anonymous}::TextDumper_Random_Test::TestBody()’:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int>, std::_Select1st<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, long long unsigned int> >, std::less<jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0> >, std::allocator<std::pair<const jellyfish::mer_dna_ns::mer_base_static<long long unsigned int, 0>, 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<const key_type&>(__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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
unit_tests/gtest/src/gtest-all.cc: In function ‘bool testing::internal::StackGrowsDown()’:
unit_tests/gtest/src/gtest-all.cc:7485:24: warning: ‘dummy’ may be used uninitialized [-Wmaybe-uninitialized]
7485 | StackLowerThanAddress(&dummy, &result);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
unit_tests/gtest/src/gtest-all.cc:7477:6: note: by argument 1 of type ‘const void*’ to ‘void testing::internal::StackLowerThanAddress(const void*, bool*)’ declared here
7477 | void StackLowerThanAddress(const void* ptr, bool* result) {
| ^~~~~~~~~~~~~~~~~~~~~
unit_tests/gtest/src/gtest-all.cc:7483:7: note: ‘dummy’ declared here
7483 | int dummy;
| ^~~~~
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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -R/<<PKGBUILDDIR>>/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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -R/<<PKGBUILDDIR>>/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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf ./.libs/libgtest.a -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<<PKGBUILDDIR>>/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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -R/<<PKGBUILDDIR>>/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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_install -- install-data
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no install-data
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make install-am
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/bin/jellyfish
/bin/mkdir -p '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
/usr/bin/install -c -m 644 'doc/jellyfish.man' '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1/jellyfish.1'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
libtool: warning: relinking 'swig/perl5/jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/5.34.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<<PKGBUILDDIR>>/debian/tmp)
libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/11/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0 && { 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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0 && { 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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.la
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.34.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/usr/bin/install -c swig/perl5/jellyfish.pm '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-2.0.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
libtool: warning: relinking 'swig/python/_dna_jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/debian/tmp)
libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/11/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.la
libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/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'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
/usr/bin/install -c swig/python/__init__.pyc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
/bin/mkdir -p '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
/usr/bin/install -c -m 644 'doc/jellyfish.man' '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1/jellyfish.1'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
libtool: warning: relinking 'swig/perl5/jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/5.34.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<<PKGBUILDDIR>>/debian/tmp)
libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/11/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0 && { 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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0 && { 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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.la
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.34.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/usr/bin/install -c swig/perl5/jellyfish.pm '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-2.0.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
libtool: warning: relinking 'swig/python/_dna_jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/debian/tmp)
libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/11/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.la
libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/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'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
/usr/bin/install -c swig/python/__init__.pyc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build --sourcedirectory=swig/perl5
cd swig/perl5 && make -j4
make[2]: Entering directory '/<<PKGBUILDDIR>>/swig/perl5'
Running Mkbootstrap for jellyfish ()
g++ -c -std=c++0x -I/<<PKGBUILDDIR>>/debian/tmp//usr/include/jellyfish-2.3.0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/5.34/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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/swig/perl5'
dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild
I: pybuild base:237: /usr/bin/python3 setup.py build build_ext -L/<<PKGBUILDDIR>>/.libs
running build
running build_py
copying dna_jellyfish.py -> /<<PKGBUILDDIR>>/.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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/swig_wrap.o -L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf -L/<<PKGBUILDDIR>>/.libs -ljellyfish-2.0 -lpthread -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_dna_jellyfish/build/_dna_jellyfish.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
chrpath --delete bin/.libs/*
dh_auto_install -- install-data
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no install-data
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make install-am
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/bin/jellyfish
/bin/mkdir -p '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
/usr/bin/install -c -m 644 'doc/jellyfish.man' '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1/jellyfish.1'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
libtool: warning: relinking 'swig/perl5/jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/5.34.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<<PKGBUILDDIR>>/debian/tmp)
libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/11/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0 && { 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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0 && { 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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.la
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.34.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/usr/bin/install -c swig/perl5/jellyfish.pm '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-2.0.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
libtool: warning: relinking 'swig/python/_dna_jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/debian/tmp)
libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/11/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.la
libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/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'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
/usr/bin/install -c swig/python/__init__.pyc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
/bin/mkdir -p '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
/usr/bin/install -c -m 644 'doc/jellyfish.man' '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1/jellyfish.1'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
libtool: warning: relinking 'swig/perl5/jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/5.34.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<<PKGBUILDDIR>>/debian/tmp)
libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/11/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0 && { 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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0 && { 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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.la
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0/jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.34.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/usr/bin/install -c swig/perl5/jellyfish.pm '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.34.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-2.0.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
libtool: warning: relinking 'swig/python/_dna_jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/debian/tmp)
libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -L/usr/lib/gcc/arm-linux-gnueabihf/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/11/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.la
libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/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'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
/usr/bin/install -c swig/python/__init__.pyc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3/dist-packages/dna_jellyfish'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild
I: pybuild base:237: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish
running install
running build
running build_py
running build_ext
running install_lib
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.9
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_dna_jellyfish/build/dna_jellyfish.py -> /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_dna_jellyfish/build/_dna_jellyfish.cpython-39-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages
byte-compiling /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.9/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-39.pyc
running install_egg_info
Writing /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr
make[2]: Entering directory '/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/perl5/5.34/auto/jellyfish/jellyfish.so
make[2]: Leaving directory '/<<PKGBUILDDIR>>/swig/perl5'
ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so
-r-xr-xr-x 1 buildd buildd 1069780 Feb 13 03:29 debian/tmp/usr/lib/arm-linux-gnueabihf/perl5/5.34/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2 debian/libjellyfish-2.0-2/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_python3 -a
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
debian/rules override_dh_missing
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# 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.*
dh_missing
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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: 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: package could avoid a useless dependency if debian/jellyfish/usr/lib/jellyfish/bin/fastq2sam debian/jellyfish/usr/lib/jellyfish/bin/generate_sequence debian/jellyfish/usr/bin/jellyfish debian/jellyfish/usr/lib/jellyfish/bin/test_all were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
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 -a
dh_gencontrol -a
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: 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 -a
dh_builddeb -a
dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.0-12+b1_armhf.deb'.
dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.0-12+b1_armhf.deb'.
dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.0-12+b1_armhf.deb'.
dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.0-12+b1_armhf.deb'.
dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.0-12+b1_armhf.deb'.
dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.0-12+b1_armhf.deb'.
dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.0-12+b1_armhf.deb'.
dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.0-12+b1_armhf.deb'.
dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.0-12+b1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../jellyfish_2.3.0-12+b1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../jellyfish_2.3.0-12+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-02-13T03:30:07Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
jellyfish_2.3.0-12+b1_armhf.changes:
------------------------------------
Format: 1.8
Date: Sun, 13 Feb 2022 03:20:25 +0000
Source: jellyfish (2.3.0-12)
Binary: jellyfish jellyfish-dbgsym libjellyfish-2.0-2 libjellyfish-2.0-2-dbgsym libjellyfish-2.0-dev libjellyfish-perl libjellyfish-perl-dbgsym python3-dna-jellyfish python3-dna-jellyfish-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 2.3.0-12+b1
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Raspbian pi4 based autobuilder <root@raspbian.org>
Description:
jellyfish - count k-mers in DNA sequences
libjellyfish-2.0-2 - count k-mers in DNA sequences (dynamic library of jellyfish)
libjellyfish-2.0-dev - count k-mers in DNA sequences (development files of jellyfish)
libjellyfish-perl - count k-mers in DNA sequences (Perl bindings of jellyfish)
python3-dna-jellyfish - count k-mers in DNA sequences (Python bindings of jellyfish)
Changes:
jellyfish (2.3.0-12+b1) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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Files:
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a1c39b2f2ebaf79c7fdecf4c260a16c2 10520 science optional jellyfish_2.3.0-12+b1_armhf.buildinfo
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dea16a1294e614ca651daad86f8ab996 57244 perl optional libjellyfish-perl_2.3.0-12+b1_armhf.deb
c9d634f7864e2d992069168fd7300702 327100 debug optional python3-dna-jellyfish-dbgsym_2.3.0-12+b1_armhf.deb
3592b65154fea43d22ca5e2f5aec5c89 54556 python optional python3-dna-jellyfish_2.3.0-12+b1_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: jellyfish (2.3.0-12)
Binary: jellyfish jellyfish-dbgsym libjellyfish-2.0-2 libjellyfish-2.0-2-dbgsym libjellyfish-2.0-dev libjellyfish-perl libjellyfish-perl-dbgsym python3-dna-jellyfish python3-dna-jellyfish-dbgsym
Architecture: armhf
Version: 2.3.0-12+b1
Binary-Only-Changes:
jellyfish (2.3.0-12+b1) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
.
-- Raspbian pi4 based autobuilder <root@raspbian.org> Sun, 13 Feb 2022 03:20:25 +0000
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sun, 13 Feb 2022 03:30:05 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
adduser (= 3.118),
apt (= 2.3.15),
autoconf (= 2.71-2),
automake (= 1:1.16.5-1.1),
autopoint (= 0.21-4),
autotools-dev (= 20220109.1),
base-files (= 12+rpi1),
base-passwd (= 3.5.52),
bash (= 5.1-6),
bc (= 1.07.1-3),
binutils (= 2.37.90.20220130-2+rpi2),
binutils-arm-linux-gnueabihf (= 2.37.90.20220130-2+rpi2),
binutils-common (= 2.37.90.20220130-2+rpi2),
bsdextrautils (= 2.37.3-1),
bsdutils (= 1:2.37.3-1),
build-essential (= 12.9),
bzip2 (= 1.0.8-5),
ca-certificates (= 20211016),
chrpath (= 0.16-2),
coreutils (= 8.32-4.1),
cpp (= 4:11.2.0-2+rpi1),
cpp-11 (= 11.2.0-14+rpi1),
d-shlibs (= 0.104),
dash (= 0.5.11+git20210903+057cd650a4ed-3),
debconf (= 1.5.79),
debhelper (= 13.6),
debianutils (= 4.11.2),
dh-autoreconf (= 20),
dh-python (= 5.20220119),
dh-strip-nondeterminism (= 1.13.0-1),
diffutils (= 1:3.7-5),
dirmngr (= 2.2.27-3),
dos2unix (= 7.4.2-2),
dpkg (= 1.21.1+rpi1),
dpkg-dev (= 1.21.1+rpi1),
dwz (= 0.14-1),
file (= 1:5.41-2),
findutils (= 4.8.0-1),
g++ (= 4:11.2.0-2+rpi1),
g++-11 (= 11.2.0-14+rpi1),
gcc (= 4:11.2.0-2+rpi1),
gcc-11 (= 11.2.0-14+rpi1),
gcc-11-base (= 11.2.0-14+rpi1),
gettext (= 0.21-4),
gettext-base (= 0.21-4),
gnupg (= 2.2.27-3),
gnupg-l10n (= 2.2.27-3),
gnupg-utils (= 2.2.27-3),
gpg (= 2.2.27-3),
gpg-agent (= 2.2.27-3),
gpg-wks-client (= 2.2.27-3),
gpg-wks-server (= 2.2.27-3),
gpgconf (= 2.2.27-3),
gpgsm (= 2.2.27-3),
gpgv (= 2.2.27-3),
grep (= 3.7-1),
groff-base (= 1.22.4-8),
gzip (= 1.10-4),
hostname (= 3.23),
init-system-helpers (= 1.61),
intltool-debian (= 0.35.0+20060710.5),
libacl1 (= 2.3.1-1),
libapt-pkg6.0 (= 2.3.15),
libarchive-zip-perl (= 1.68-1),
libasan6 (= 11.2.0-14+rpi1),
libassuan0 (= 2.5.5-1),
libatomic1 (= 11.2.0-14+rpi1),
libattr1 (= 1:2.5.1-1),
libaudit-common (= 1:3.0.6-1),
libaudit1 (= 1:3.0.6-1),
libbinutils (= 2.37.90.20220130-2+rpi2),
libblkid1 (= 2.37.3-1),
libbrotli1 (= 1.0.9-2+b1),
libbsd0 (= 0.11.5-1),
libbz2-1.0 (= 1.0.8-5),
libc-bin (= 2.33-5+rpi1),
libc-dev-bin (= 2.33-5+rpi1),
libc6 (= 2.33-5+rpi1),
libc6-dev (= 2.33-5+rpi1),
libcap-ng0 (= 0.7.9-2.2+b1),
libcap2 (= 1:2.44-1),
libcc1-0 (= 11.2.0-14+rpi1),
libcom-err2 (= 1.46.5-2),
libcrypt-dev (= 1:4.4.27-1.1),
libcrypt1 (= 1:4.4.27-1.1),
libctf-nobfd0 (= 2.37.90.20220130-2+rpi2),
libctf0 (= 2.37.90.20220130-2+rpi2),
libcurl3-gnutls (= 7.81.0-1),
libcurl4-gnutls-dev (= 7.81.0-1),
libdb5.3 (= 5.3.28+dfsg1-0.8),
libdebconfclient0 (= 0.261),
libdebhelper-perl (= 13.6),
libdeflate-dev (= 1.8-1),
libdeflate0 (= 1.8-1),
libdpkg-perl (= 1.21.1+rpi1),
libedit2 (= 3.1-20210910-1),
libelf1 (= 0.186-1),
libexpat1 (= 2.4.4-1),
libexpat1-dev (= 2.4.4-1),
libffi8 (= 3.4.2-4),
libfile-stripnondeterminism-perl (= 1.13.0-1),
libgcc-11-dev (= 11.2.0-14+rpi1),
libgcc-s1 (= 11.2.0-14+rpi1),
libgcrypt20 (= 1.9.4-5),
libgdbm-compat4 (= 1.23-1),
libgdbm6 (= 1.23-1),
libglib2.0-0 (= 2.70.3-1),
libgmp10 (= 2:6.2.1+dfsg-3),
libgnutls30 (= 3.7.3-4),
libgomp1 (= 11.2.0-14+rpi1),
libgpg-error0 (= 1.43-3),
libgssapi-krb5-2 (= 1.18.3-7),
libhogweed6 (= 3.7.3-1),
libhts-dev (= 1.13+ds-2),
libhts3 (= 1.13+ds-2),
libhtscodecs2 (= 1.1.1-3),
libicu67 (= 67.1-7),
libidn2-0 (= 2.3.2-2),
libisl23 (= 0.24-2),
libjs-jquery (= 3.5.1+dfsg+~3.5.5-8),
libjs-sphinxdoc (= 4.3.2-1),
libjs-underscore (= 1.13.2~dfsg-2),
libk5crypto3 (= 1.18.3-7),
libkeyutils1 (= 1.6.1-2),
libkrb5-3 (= 1.18.3-7),
libkrb5support0 (= 1.18.3-7),
libksba8 (= 1.6.0-2),
libldap-2.4-2 (= 2.4.59+dfsg-1),
liblz4-1 (= 1.9.3-2),
liblzma-dev (= 5.2.5-2),
liblzma5 (= 5.2.5-2),
libmagic-mgc (= 1:5.41-2),
libmagic1 (= 1:5.41-2),
libmd0 (= 1.0.4-1),
libmount1 (= 2.37.3-1),
libmpc3 (= 1.2.1-1),
libmpdec3 (= 2.5.1-2+rpi1),
libmpfr6 (= 4.1.0-3),
libncurses6 (= 6.3-2),
libncursesw6 (= 6.3-2),
libnettle8 (= 3.7.3-1),
libnghttp2-14 (= 1.43.0-1),
libnpth0 (= 1.6-3),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.24.0-6),
libpam-modules (= 1.4.0-11),
libpam-modules-bin (= 1.4.0-11),
libpam-runtime (= 1.4.0-11),
libpam0g (= 1.4.0-11),
libpcre2-8-0 (= 10.39-3),
libpcre3 (= 2:8.39-13),
libperl5.34 (= 5.34.0-3),
libpipeline1 (= 1.5.5-1),
libprocps8 (= 2:3.3.17-6),
libpsl5 (= 0.21.0-1.2),
libpython3-all-dev (= 3.9.7-1+b4),
libpython3-dev (= 3.9.7-1+b4),
libpython3-stdlib (= 3.9.7-1+b4),
libpython3.9 (= 3.9.10-1+rpi1),
libpython3.9-dev (= 3.9.10-1+rpi1),
libpython3.9-minimal (= 3.9.10-1+rpi1),
libpython3.9-stdlib (= 3.9.10-1+rpi1),
libreadline8 (= 8.1.2-1),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libruby2.7 (= 2.7.4-1+b1),
libsasl2-2 (= 2.1.27+dfsg2-3),
libsasl2-modules-db (= 2.1.27+dfsg2-3),
libseccomp2 (= 2.5.3-2+rpi1),
libselinux1 (= 3.3-1),
libsemanage-common (= 3.3-1),
libsemanage2 (= 3.3-1),
libsepol2 (= 3.3-1),
libsigsegv2 (= 2.14-1),
libsmartcols1 (= 2.37.3-1),
libsqlite3-0 (= 3.37.2-2),
libssh2-1 (= 1.10.0-2),
libssl1.1 (= 1.1.1m-1),
libstdc++-11-dev (= 11.2.0-14+rpi1),
libstdc++6 (= 11.2.0-14+rpi1),
libsub-override-perl (= 0.09-2),
libsystemd0 (= 250.3-2+rpi1),
libtasn1-6 (= 4.18.0-4),
libtinfo6 (= 6.3-2),
libtirpc-common (= 1.3.2-2),
libtirpc-dev (= 1.3.2-2),
libtirpc3 (= 1.3.2-2),
libtool (= 2.4.6-15),
libubsan1 (= 11.2.0-14+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 250.3-2+rpi1),
libunistring2 (= 1.0-1),
libuuid1 (= 2.37.3-1),
libxml2 (= 2.9.12+dfsg-5),
libxxhash0 (= 0.8.0-2+rpi1),
libyaml-0-2 (= 0.2.2-1),
libzstd1 (= 1.4.8+dfsg-3+rpi1),
linux-libc-dev (= 5.14.16-1+rpi1),
login (= 1:4.11.1+dfsg1-1),
lsb-base (= 11.1.0+rpi1),
m4 (= 1.4.18-5),
make (= 4.3-4.1),
man-db (= 2.10.0-2),
mawk (= 1.3.4.20200120-3),
media-types (= 5.0.0),
ncurses-base (= 6.3-2),
ncurses-bin (= 6.3-2),
openssl (= 1.1.1m-1),
passwd (= 1:4.11.1+dfsg1-1),
patch (= 2.7.6-7),
perl (= 5.34.0-3),
perl-base (= 5.34.0-3),
perl-modules-5.34 (= 5.34.0-3),
pinentry-curses (= 1.1.0-4),
pkg-config (= 0.29.2-1),
po-debconf (= 1.0.21+nmu1),
procps (= 2:3.3.17-6),
python3 (= 3.9.7-1+b4),
python3-all (= 3.9.7-1+b4),
python3-all-dev (= 3.9.7-1+b4),
python3-dev (= 3.9.7-1+b4),
python3-distutils (= 3.9.10-1),
python3-lib2to3 (= 3.9.10-1),
python3-minimal (= 3.9.7-1+b4),
python3.9 (= 3.9.10-1+rpi1),
python3.9-dev (= 3.9.10-1+rpi1),
python3.9-minimal (= 3.9.10-1+rpi1),
rake (= 13.0.6-2),
raspbian-archive-keyring (= 20120528.2),
readline-common (= 8.1.2-1),
rpcsvc-proto (= 1.4.2-4),
ruby (= 1:2.7.6),
ruby-minitest (= 5.13.0-2),
ruby-net-telnet (= 0.1.1-2),
ruby-power-assert (= 1.1.7-2),
ruby-rubygems (= 3.3.5-2),
ruby-test-unit (= 3.3.9-1),
ruby-xmlrpc (= 0.3.2-1),
ruby2.7 (= 2.7.4-1+b1),
rubygems-integration (= 1.18),
samtools (= 1.13-4),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
swig (= 4.0.2-2),
swig4.0 (= 4.0.2-2),
sysvinit-utils (= 3.01-1),
tar (= 1.34+dfsg-1),
time (= 1.9-0.1),
tzdata (= 2021e-1),
util-linux (= 2.37.3-1),
xz-utils (= 5.2.5-2),
yaggo (= 1.5.10-5),
zlib1g (= 1:1.2.11.dfsg-2),
zlib1g-dev (= 1:1.2.11.dfsg-2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1644722425"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
jellyfish-dbgsym_2.3.0-12+b1_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 7069152 bytes: control archive=764 bytes.
521 bytes, 12 lines control
513 bytes, 5 lines md5sums
Package: jellyfish-dbgsym
Source: jellyfish (2.3.0-12)
Version: 2.3.0-12+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7572
Depends: jellyfish (= 2.3.0-12+b1)
Section: debug
Priority: optional
Description: debug symbols for jellyfish
Build-Ids: 46276c37778b58a32729d69a8ae464bf39772d63 8982b772cc0bc70245e2b59e5462b2a40ddce83f 9c4f327b15015779e92fafe9cb9d5eff0573b60e d251a149240a5d50cb882799a416527e308b1430
drwxr-xr-x root/root 0 2022-02-13 03:20 ./
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/.build-id/46/
-rw-r--r-- root/root 81100 2022-02-13 03:20 ./usr/lib/debug/.build-id/46/276c37778b58a32729d69a8ae464bf39772d63.debug
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/.build-id/89/
-rw-r--r-- root/root 78216 2022-02-13 03:20 ./usr/lib/debug/.build-id/89/82b772cc0bc70245e2b59e5462b2a40ddce83f.debug
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root 1435264 2022-02-13 03:20 ./usr/lib/debug/.build-id/9c/4f327b15015779e92fafe9cb9d5eff0573b60e.debug
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/.build-id/d2/
-rw-r--r-- root/root 6057180 2022-02-13 03:20 ./usr/lib/debug/.build-id/d2/51a149240a5d50cb882799a416527e308b1430.debug
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 83920 2022-02-13 03:20 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/jellyfish.debug
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-02-13 03:20 ./usr/share/doc/jellyfish-dbgsym -> jellyfish
jellyfish_2.3.0-12+b1_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 623404 bytes: control archive=1356 bytes.
1261 bytes, 26 lines control
916 bytes, 13 lines md5sums
Package: jellyfish
Source: jellyfish (2.3.0-12)
Version: 2.3.0-12+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1716
Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.5), libhts3 (>= 1.10), libjellyfish-2.0-2 (= 2.3.0-12+b1), libstdc++6 (>= 11)
Breaks: jellyfish-examples (<< 2.3.0-7)
Replaces: jellyfish-examples (<< 2.3.0-7)
Section: science
Priority: optional
Homepage: https://github.com/gmarcais/Jellyfish
Description: count k-mers in DNA sequences
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
drwxr-xr-x root/root 0 2022-02-13 03:20 ./
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/bin/
-rwxr-xr-x root/root 282716 2022-02-13 03:20 ./usr/bin/jellyfish
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/jellyfish/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/jellyfish/bin/
-rwxr-xr-x root/root 22228 2022-02-13 03:20 ./usr/lib/jellyfish/bin/fastq2sam
-rwxr-xr-x root/root 26420 2022-02-13 03:20 ./usr/lib/jellyfish/bin/generate_sequence
-rwxr-xr-x root/root 1165080 2022-02-13 03:20 ./usr/lib/jellyfish/bin/test_all
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc-base/
-rw-r--r-- root/root 987 2021-08-31 07:16 ./usr/share/doc-base/jellyfish.jellyfish
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/jellyfish/
-rw-r--r-- root/root 321 2021-08-31 07:16 ./usr/share/doc/jellyfish/README.test
-rw-r--r-- root/root 221 2022-02-13 03:20 ./usr/share/doc/jellyfish/changelog.Debian.armhf.gz
-rw-r--r-- root/root 4342 2022-02-13 03:20 ./usr/share/doc/jellyfish/changelog.Debian.gz
-rw-r--r-- root/root 284 2019-07-13 12:16 ./usr/share/doc/jellyfish/changelog.gz
-rw-r--r-- root/root 6321 2021-08-31 07:16 ./usr/share/doc/jellyfish/copyright
-rw-r--r-- root/root 221453 2019-07-13 12:16 ./usr/share/doc/jellyfish/jellyfish.pdf.gz
-rw-r--r-- root/root 1665 2021-08-31 07:16 ./usr/share/doc/jellyfish/run-unit-test
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/man/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/man/man1/
-rw-r--r-- root/root 4554 2022-02-13 03:20 ./usr/share/man/man1/jellyfish.1.gz
libjellyfish-2.0-2-dbgsym_2.3.0-12+b1_armhf.deb
-----------------------------------------------
new Debian package, version 2.0.
size 537224 bytes: control archive=568 bytes.
441 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libjellyfish-2.0-2-dbgsym
Source: jellyfish (2.3.0-12)
Version: 2.3.0-12+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 567
Depends: libjellyfish-2.0-2 (= 2.3.0-12+b1)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libjellyfish-2.0-2
Build-Ids: 1ef522427344e977438efa81e30f68ee2c635f41
drwxr-xr-x root/root 0 2022-02-13 03:20 ./
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/.build-id/1e/
-rw-r--r-- root/root 569884 2022-02-13 03:20 ./usr/lib/debug/.build-id/1e/f522427344e977438efa81e30f68ee2c635f41.debug
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-02-13 03:20 ./usr/share/doc/libjellyfish-2.0-2-dbgsym -> libjellyfish-2.0-2
libjellyfish-2.0-2_2.3.0-12+b1_armhf.deb
----------------------------------------
new Debian package, version 2.0.
size 56552 bytes: control archive=1284 bytes.
1270 bytes, 28 lines control
506 bytes, 6 lines md5sums
49 bytes, 1 lines shlibs
65 bytes, 2 lines triggers
Package: libjellyfish-2.0-2
Source: jellyfish (2.3.0-12)
Version: 2.3.0-12+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 162
Depends: libc6 (>= 2.7), libgcc-s1 (>= 3.5), libstdc++6 (>= 11)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/gmarcais/Jellyfish
Description: count k-mers in DNA sequences (dynamic library of jellyfish)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
.
This package contains the dynamic library the main executable of
jellyfish is linked to.
drwxr-xr-x root/root 0 2022-02-13 03:20 ./
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2 -> libjellyfish-2.0.so.2.0.0
-rw-r--r-- root/root 136612 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so.2.0.0
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/libjellyfish-2.0-2/
-rw-r--r-- root/root 221 2022-02-13 03:20 ./usr/share/doc/libjellyfish-2.0-2/changelog.Debian.armhf.gz
-rw-r--r-- root/root 4342 2022-02-13 03:20 ./usr/share/doc/libjellyfish-2.0-2/changelog.Debian.gz
-rw-r--r-- root/root 284 2019-07-13 12:16 ./usr/share/doc/libjellyfish-2.0-2/changelog.gz
-rw-r--r-- root/root 6321 2021-08-31 07:16 ./usr/share/doc/libjellyfish-2.0-2/copyright
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/lintian/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 230 2021-08-31 07:16 ./usr/share/lintian/overrides/libjellyfish-2.0-2
libjellyfish-2.0-dev_2.3.0-12+b1_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 128700 bytes: control archive=2568 bytes.
1230 bytes, 27 lines control
4352 bytes, 58 lines md5sums
Package: libjellyfish-2.0-dev
Source: jellyfish (2.3.0-12)
Version: 2.3.0-12+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 604
Depends: libjellyfish-2.0-2 (= 2.3.0-12+b1)
Section: libdevel
Priority: optional
Homepage: https://github.com/gmarcais/Jellyfish
Description: count k-mers in DNA sequences (development files of jellyfish)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
.
This package contains the development files (static library and
header files)
drwxr-xr-x root/root 0 2022-02-13 03:20 ./
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/include/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/include/jellyfish/
-rw-r--r-- root/root 1596 2022-02-13 03:20 ./usr/include/jellyfish/allocators_mmap.hpp
-rw-r--r-- root/root 5898 2022-02-13 03:20 ./usr/include/jellyfish/atomic_bits_array.hpp
-rw-r--r-- root/root 4770 2022-02-13 03:20 ./usr/include/jellyfish/atomic_field.hpp
-rw-r--r-- root/root 1392 2022-02-13 03:20 ./usr/include/jellyfish/atomic_gcc.hpp
-rw-r--r-- root/root 272 2022-02-13 03:20 ./usr/include/jellyfish/backtrace.hpp
-rw-r--r-- root/root 6829 2022-02-13 03:20 ./usr/include/jellyfish/binary_dumper.hpp
-rw-r--r-- root/root 3480 2022-02-13 03:20 ./usr/include/jellyfish/bloom_common.hpp
-rw-r--r-- root/root 6778 2022-02-13 03:20 ./usr/include/jellyfish/bloom_counter2.hpp
-rw-r--r-- root/root 5447 2022-02-13 03:20 ./usr/include/jellyfish/bloom_filter.hpp
-rw-r--r-- root/root 5211 2022-02-13 03:20 ./usr/include/jellyfish/circular_buffer.hpp
-rw-r--r-- root/root 2408 2022-02-13 03:20 ./usr/include/jellyfish/compare_and_swap.hpp
-rw-r--r-- root/root 5861 2022-02-13 03:20 ./usr/include/jellyfish/config.h
-rw-r--r-- root/root 7472 2022-02-13 03:20 ./usr/include/jellyfish/cooperative_pool.hpp
-rw-r--r-- root/root 8494 2022-02-13 03:20 ./usr/include/jellyfish/cooperative_pool2.hpp
-rw-r--r-- root/root 4125 2022-02-13 03:20 ./usr/include/jellyfish/cpp_array.hpp
-rw-r--r-- root/root 2742 2022-02-13 03:20 ./usr/include/jellyfish/divisor.hpp
-rw-r--r-- root/root 2710 2022-02-13 03:20 ./usr/include/jellyfish/dumper.hpp
-rw-r--r-- root/root 2257 2022-02-13 03:20 ./usr/include/jellyfish/err.hpp
-rw-r--r-- root/root 4033 2022-02-13 03:20 ./usr/include/jellyfish/file_header.hpp
-rw-r--r-- root/root 4637 2022-02-13 03:20 ./usr/include/jellyfish/generator_manager.hpp
-rw-r--r-- root/root 6814 2022-02-13 03:20 ./usr/include/jellyfish/generic_file_header.hpp
-rw-r--r-- root/root 8326 2022-02-13 03:20 ./usr/include/jellyfish/hash_counter.hpp
-rw-r--r-- root/root 7025 2022-02-13 03:20 ./usr/include/jellyfish/int128.hpp
-rw-r--r-- root/root 1118 2022-02-13 03:20 ./usr/include/jellyfish/jellyfish.hpp
-rw-r--r-- root/root 61697 2022-02-13 03:20 ./usr/include/jellyfish/json.h
-rw-r--r-- root/root 40578 2022-02-13 03:20 ./usr/include/jellyfish/large_hash_array.hpp
-rw-r--r-- root/root 7564 2022-02-13 03:20 ./usr/include/jellyfish/large_hash_iterator.hpp
-rw-r--r-- root/root 4328 2022-02-13 03:20 ./usr/include/jellyfish/locks_pthread.hpp
-rw-r--r-- root/root 5181 2022-02-13 03:20 ./usr/include/jellyfish/mapped_file.hpp
-rw-r--r-- root/root 23866 2022-02-13 03:20 ./usr/include/jellyfish/mer_dna.hpp
-rw-r--r-- root/root 1296 2022-02-13 03:20 ./usr/include/jellyfish/mer_dna_bloom_counter.hpp
-rw-r--r-- root/root 3076 2022-02-13 03:20 ./usr/include/jellyfish/mer_heap.hpp
-rw-r--r-- root/root 2588 2022-02-13 03:20 ./usr/include/jellyfish/mer_iterator.hpp
-rw-r--r-- root/root 9371 2022-02-13 03:20 ./usr/include/jellyfish/mer_overlap_sequence_parser.hpp
-rw-r--r-- root/root 3247 2022-02-13 03:20 ./usr/include/jellyfish/mer_qual_iterator.hpp
-rw-r--r-- root/root 8066 2022-02-13 03:20 ./usr/include/jellyfish/misc.hpp
-rw-r--r-- root/root 10025 2022-02-13 03:20 ./usr/include/jellyfish/offsets_key_value.hpp
-rw-r--r-- root/root 960 2022-02-13 03:20 ./usr/include/jellyfish/parser_common.hpp
-rw-r--r-- root/root 12884 2022-02-13 03:20 ./usr/include/jellyfish/rectangular_binary_matrix.hpp
-rw-r--r-- root/root 2311 2022-02-13 03:20 ./usr/include/jellyfish/sam_format.hpp
-rw-r--r-- root/root 3504 2022-02-13 03:20 ./usr/include/jellyfish/simple_circular_buffer.hpp
-rw-r--r-- root/root 3407 2022-02-13 03:20 ./usr/include/jellyfish/sorted_dumper.hpp
-rw-r--r-- root/root 5069 2022-02-13 03:20 ./usr/include/jellyfish/stdio_filebuf.hpp
-rw-r--r-- root/root 602 2022-02-13 03:20 ./usr/include/jellyfish/storage.hpp
-rw-r--r-- root/root 2036 2022-02-13 03:20 ./usr/include/jellyfish/stream_iterator.hpp
-rw-r--r-- root/root 6318 2022-02-13 03:20 ./usr/include/jellyfish/stream_manager.hpp
-rw-r--r-- root/root 2063 2022-02-13 03:20 ./usr/include/jellyfish/text_dumper.hpp
-rw-r--r-- root/root 994 2022-02-13 03:20 ./usr/include/jellyfish/thread_exec.hpp
-rw-r--r-- root/root 1884 2022-02-13 03:20 ./usr/include/jellyfish/time.hpp
-rw-r--r-- root/root 1599 2022-02-13 03:20 ./usr/include/jellyfish/token_ring.hpp
-rw-r--r-- root/root 6761 2022-02-13 03:20 ./usr/include/jellyfish/whole_sequence_parser.hpp
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 220334 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.a
-rw-r--r-- root/root 1009 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.la
lrwxrwxrwx root/root 0 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so -> libjellyfish-2.0.so.2.0.0
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 276 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/pkgconfig/jellyfish-2.0.pc
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/libjellyfish-2.0-dev/
-rw-r--r-- root/root 221 2022-02-13 03:20 ./usr/share/doc/libjellyfish-2.0-dev/changelog.Debian.armhf.gz
-rw-r--r-- root/root 4342 2022-02-13 03:20 ./usr/share/doc/libjellyfish-2.0-dev/changelog.Debian.gz
-rw-r--r-- root/root 284 2019-07-13 12:16 ./usr/share/doc/libjellyfish-2.0-dev/changelog.gz
-rw-r--r-- root/root 6321 2021-08-31 07:16 ./usr/share/doc/libjellyfish-2.0-dev/copyright
libjellyfish-perl-dbgsym_2.3.0-12+b1_armhf.deb
----------------------------------------------
new Debian package, version 2.0.
size 344516 bytes: control archive=568 bytes.
438 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libjellyfish-perl-dbgsym
Source: jellyfish (2.3.0-12)
Version: 2.3.0-12+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 370
Depends: libjellyfish-perl (= 2.3.0-12+b1)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libjellyfish-perl
Build-Ids: 45b96fa1d24972f0541f3d2a97c192f5395c5ee6
drwxr-xr-x root/root 0 2022-02-13 03:20 ./
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/
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drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/debug/.build-id/45/
-rw-r--r-- root/root 368148 2022-02-13 03:20 ./usr/lib/debug/.build-id/45/b96fa1d24972f0541f3d2a97c192f5395c5ee6.debug
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-02-13 03:20 ./usr/share/doc/libjellyfish-perl-dbgsym -> libjellyfish-perl
libjellyfish-perl_2.3.0-12+b1_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 57244 bytes: control archive=1160 bytes.
1234 bytes, 27 lines control
497 bytes, 6 lines md5sums
Package: libjellyfish-perl
Source: jellyfish (2.3.0-12)
Version: 2.3.0-12+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 173
Depends: perl, perlapi-5.34.0, libc6 (>= 2.33), libgcc-s1 (>= 3.5)
Section: perl
Priority: optional
Multi-Arch: same
Homepage: https://github.com/gmarcais/Jellyfish
Description: count k-mers in DNA sequences (Perl bindings of jellyfish)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
.
This package contains the Perl bindings of jellyfish.
drwxr-xr-x root/root 0 2022-02-13 03:20 ./
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/
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drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/perl5/5.34/auto/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/perl5/5.34/auto/jellyfish/
-rw-r--r-- root/root 141252 2022-02-13 03:20 ./usr/lib/arm-linux-gnueabihf/perl5/5.34/auto/jellyfish/jellyfish.so
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/
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drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/libjellyfish-perl/
-rw-r--r-- root/root 221 2022-02-13 03:20 ./usr/share/doc/libjellyfish-perl/changelog.Debian.armhf.gz
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-rw-r--r-- root/root 6321 2021-08-31 07:16 ./usr/share/doc/libjellyfish-perl/copyright
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/perl5/
-rw-r--r-- root/root 7412 2022-02-13 03:20 ./usr/share/perl5/jellyfish.pm
python3-dna-jellyfish-dbgsym_2.3.0-12+b1_armhf.deb
--------------------------------------------------
new Debian package, version 2.0.
size 327100 bytes: control archive=556 bytes.
433 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: python3-dna-jellyfish-dbgsym
Source: jellyfish (2.3.0-12)
Version: 2.3.0-12+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 356
Depends: python3-dna-jellyfish (= 2.3.0-12+b1)
Section: debug
Priority: optional
Description: debug symbols for python3-dna-jellyfish
Build-Ids: 2cdde87ee2b54bc2d5f16b5d3a08b1bd51209ff7
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-rw-r--r-- root/root 354272 2022-02-13 03:20 ./usr/lib/debug/.build-id/2c/dde87ee2b54bc2d5f16b5d3a08b1bd51209ff7.debug
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-02-13 03:20 ./usr/share/doc/python3-dna-jellyfish-dbgsym -> python3-dna-jellyfish
python3-dna-jellyfish_2.3.0-12+b1_armhf.deb
-------------------------------------------
new Debian package, version 2.0.
size 54556 bytes: control archive=1540 bytes.
1308 bytes, 26 lines control
636 bytes, 7 lines md5sums
279 bytes, 12 lines * postinst #!/bin/sh
428 bytes, 12 lines * prerm #!/bin/sh
Package: python3-dna-jellyfish
Source: jellyfish (2.3.0-12)
Version: 2.3.0-12+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 167
Depends: python3 (<< 3.10), python3 (>= 3.9~), python3:any, libc6 (>= 2.33), libgcc-s1 (>= 3.5), libjellyfish-2.0-2 (>= 2.3.0), libstdc++6 (>= 5.2)
Section: python
Priority: optional
Homepage: https://github.com/gmarcais/Jellyfish
Description: count k-mers in DNA sequences (Python bindings of jellyfish)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
.
This package contains the Python bindings of jellyfish.
drwxr-xr-x root/root 0 2022-02-13 03:20 ./
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/python3/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/lib/python3/dist-packages/
-rw-r--r-- root/root 130536 2022-02-13 03:20 ./usr/lib/python3/dist-packages/_dna_jellyfish.cpython-39-arm-linux-gnueabihf.so
-rw-r--r-- root/root 224 2022-02-13 03:20 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info
-rw-r--r-- root/root 12878 2022-02-13 03:20 ./usr/lib/python3/dist-packages/dna_jellyfish.py
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-02-13 03:20 ./usr/share/doc/python3-dna-jellyfish/
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-rw-r--r-- root/root 4342 2022-02-13 03:20 ./usr/share/doc/python3-dna-jellyfish/changelog.Debian.gz
-rw-r--r-- root/root 284 2019-07-13 12:16 ./usr/share/doc/python3-dna-jellyfish/changelog.gz
-rw-r--r-- root/root 6321 2021-08-31 07:16 ./usr/share/doc/python3-dna-jellyfish/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 134264
Build-Time: 582
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 617
Job: jellyfish_2.3.0-12
Machine Architecture: armhf
Package: jellyfish
Package-Time: 1227
Source-Version: 2.3.0-12
Space: 134264
Status: successful
Version: 2.3.0-12+b1
--------------------------------------------------------------------------------
Finished at 2022-02-13T03:30:07Z
Build needed 00:20:27, 134264k disk space