[Debian-med-packaging] Bug#1022087: jellyfish: FTBFS with pkgconf
Andrej Shadura
andrewsh at debian.org
Wed Oct 19 21:11:12 BST 2022
Source: jellyfish
Version: 2.3.0-15
Severity: normal
Tags: ftbfs
User: andrewsh at debian.org
Usertags: pkgconf-rebuild-ftbfs
Dear Maintainer,
While rebuilding your package with pkgconf instead of pkg-config, your
package failed to build from the source at the build stage
due to the following error:
Missing C Header: jellyfish/mer_dna.hpp
These log lines may help you identify the reason:
...
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish'
/usr/bin/install -c swig/python/__init__.pyc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build --sourcedirectory=swig/perl5
cd swig/perl5 && make -j3
make[2]: Entering directory '/<<PKGBUILDDIR>>/swig/perl5'
Running Mkbootstrap for jellyfish ()
chmod 644 "jellyfish.bs"
g++ -c -std=c++0x -I/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/x86_64-linux-gnu/perl/5.36/CORE" swig_wrap.cpp
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644
> swig_wrap.cpp:1609:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory
1609 | #include <jellyfish/mer_dna.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [Makefile:342: swig_wrap.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/swig/perl5'
dh_auto_build: error: cd swig/perl5 && make -j3 returned exit code 2
make[1]: *** [debian/rules:87: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:22: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
To reproduce the failure, use this command:
sbuild -d unstable --add-depends=pkgconf jellyfish
The full build log is attached for your reference.
Please note that this email has been generated semi-automatically.
--
Thanks,
Andrej
-------------- next part --------------
sbuild (Debian sbuild) 0.83.2 (29 August 2022) on scw-hardcore-ride
+==============================================================================+
| jellyfish (amd64) Wed, 19 Oct 2022 15:12:36 +0000 |
+==============================================================================+
Package: jellyfish
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: binary
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-ec7a321c-e863-4830-b3d0-41cf13e7abb2' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/jellyfish-SUMaco/resolver-GIfBU2' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://deb.debian.org/debian unstable InRelease [161 kB]
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Get:5 http://deb.debian.org/debian unstable/main amd64 Packages [9372 kB]
Fetched 19.6 MB in 2s (9429 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Calculating upgrade...
The following NEW packages will be installed:
libperl5.36 perl-modules-5.36
The following packages will be upgraded:
adduser apt base-files base-passwd bash binutils binutils-common
binutils-x86-64-linux-gnu bsdutils bzip2 ccache coreutils cpp-12 dirmngr
dpkg e2fsprogs g++-12 gcc-12 gcc-12-base gnupg gnupg-l10n gnupg-utils gpg
gpg-agent gpg-wks-client gpg-wks-server gpgconf gpgsm gpgv grep
init-system-helpers libapt-pkg6.0 libasan8 libatomic1 libaudit-common
libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6
libc6-dev libcc1-0 libcom-err2 libctf-nobfd0 libctf0 libeatmydata1
libext2fs2 libffi8 libgcc-12-dev libgcc-s1 libgdbm-compat4 libgdbm6 libgmp10
libgnutls30 libgomp1 libgprofng0 libgssapi-krb5-2 libitm1 libk5crypto3
libkrb5-3 libkrb5support0 libksba8 libldap-2.5-0 liblsan0 libmount1
libpam-modules libpam-modules-bin libpam-runtime libpam0g libquadmath0
libreadline8 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage2
libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6
libsystemd0 libtasn1-6 libtsan2 libubsan1 libudev1 libunistring2 libuuid1
linux-libc-dev login logsave lsb-base mount passwd perl perl-base
pinentry-curses readline-common sysvinit-utils tzdata usr-is-merged
util-linux util-linux-extra
105 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
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+------------------------------------------------------------------------------+
| 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 698 kB of source archives.
Get:1 http://deb.debian.org/debian unstable/main jellyfish 2.3.0-15 (dsc) [3224 B]
Get:2 http://deb.debian.org/debian unstable/main jellyfish 2.3.0-15 (tar) [679 kB]
Get:3 http://deb.debian.org/debian unstable/main jellyfish 2.3.0-15 (diff) [15.4 kB]
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Download complete and in download only mode
W: Download is performed unsandboxed as root as file 'jellyfish_2.3.0-15.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied)
I: NOTICE: Log filtering will replace 'build/jellyfish-SUMaco/jellyfish-2.3.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/jellyfish-SUMaco' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), d-shlibs, autoconf-archive, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools, pkgconf, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), d-shlibs, autoconf-archive, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools, pkgconf, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
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Reading package lists...
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Install main build dependencies (apt-based resolver)
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Installing build dependencies
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Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf autoconf-archive 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 libhts-dev
libhts3 libhtscodecs2 libicu71 libjs-jquery libjs-sphinxdoc libjs-underscore
liblzma-dev libmagic-mgc libmagic1 libmd0 libmpdec3 libncurses6
libnghttp2-14 libpipeline1 libpkgconf3 libprocps8 libpsl5 libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev
libpython3.10-minimal libpython3.10-stdlib librtmp1 libruby libruby3.0
libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4
man-db media-types openssl pkgconf pkgconf-bin po-debconf procps python3
python3-all python3-all-dev python3-dev python3-distutils python3-lib2to3
python3-minimal python3.10 python3.10-dev python3.10-minimal rake ruby
ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.0
rubygems-integration samtools sensible-utils swig swig4.0 time yaggo
zlib1g-dev
Suggested packages:
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 python3.10-venv
python3.10-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 javascript-common libgpm2
publicsuffix libltdl-dev libmail-sendmail-perl psmisc zip fonts-lato
The following NEW packages will be installed:
autoconf autoconf-archive 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 libhts-dev
libhts3 libhtscodecs2 libicu71 libjs-jquery libjs-sphinxdoc libjs-underscore
liblzma-dev libmagic-mgc libmagic1 libmd0 libmpdec3 libncurses6
libnghttp2-14 libpipeline1 libpkgconf3 libprocps8 libpsl5 libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev
libpython3.10-minimal libpython3.10-stdlib librtmp1 libruby libruby3.0
libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4
man-db media-types openssl pkgconf pkgconf-bin po-debconf procps python3
python3-all python3-all-dev python3-dev python3-distutils python3-lib2to3
python3-minimal python3.10 python3.10-dev python3.10-minimal rake ruby
ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.0
rubygems-integration samtools sbuild-build-depends-main-dummy sensible-utils
swig swig4.0 time yaggo zlib1g-dev
0 upgraded, 103 newly installed, 0 to remove and 0 not upgraded.
Need to get 48.7 MB of archives.
After this operation, 185 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [972 B]
Get:2 http://deb.debian.org/debian unstable/main amd64 autoconf-archive all 20220903-2 [779 kB]
Get:3 http://deb.debian.org/debian unstable/main amd64 libpython3.10-minimal amd64 3.10.7-2 [828 kB]
Get:4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.4.9-1 [105 kB]
Get:5 http://deb.debian.org/debian unstable/main amd64 python3.10-minimal amd64 3.10.7-2 [1994 kB]
Get:6 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.10.6-1 [38.7 kB]
Get:7 http://deb.debian.org/debian unstable/main amd64 media-types all 8.0.0 [33.4 kB]
Get:8 http://deb.debian.org/debian unstable/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB]
Get:9 http://deb.debian.org/debian unstable/main amd64 libpython3.10-stdlib amd64 3.10.7-2 [1684 kB]
Get:10 http://deb.debian.org/debian unstable/main amd64 python3.10 amd64 3.10.7-2 [547 kB]
Get:11 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.10.6-1 [21.7 kB]
Get:12 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.10.6-1 [38.2 kB]
Get:13 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.3+20220423-2 [102 kB]
Get:14 http://deb.debian.org/debian unstable/main amd64 libprocps8 amd64 2:3.3.17-7+b1 [64.2 kB]
Get:15 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:3.3.17-7+b1 [502 kB]
Get:16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.17 [21.5 kB]
Get:17 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.0.5-4 [1423 kB]
Get:18 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20211016 [156 kB]
Get:19 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.41-4 [295 kB]
Get:20 http://deb.debian.org/debian unstable/main amd64 libmagic1 amd64 1:5.41-4 [129 kB]
Get:21 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.41-4 [67.0 kB]
Get:22 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-9 [175 kB]
Get:23 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get:24 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.22.4-8 [936 kB]
Get:25 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.38.1-1.1+b1 [85.9 kB]
Get:26 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.6-3 [39.4 kB]
Get:27 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.11.0-1+b1 [1342 kB]
Get:28 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-1 [291 kB]
Get:29 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-2 [343 kB]
Get:30 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:31 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:32 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-9 [510 kB]
Get:33 http://deb.debian.org/debian unstable/main amd64 bc amd64 1.07.1-3+b1 [110 kB]
Get:34 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB]
Get:35 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.104 [18.6 kB]
Get:36 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.10 [79.8 kB]
Get:37 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-4 [526 kB]
Get:38 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:39 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:40 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get:41 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:42 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:43 http://deb.debian.org/debian unstable/main amd64 libelf1 amd64 0.187-4 [179 kB]
Get:44 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.14+20220924-2 [109 kB]
Get:45 http://deb.debian.org/debian unstable/main amd64 libicu71 amd64 71.1-3 [9218 kB]
Get:46 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1+b1 [708 kB]
Get:47 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-9 [1315 kB]
Get:48 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:49 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:50 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.10 [940 kB]
Get:51 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.10.7-1 [79.9 kB]
Get:52 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.10.7-1 [141 kB]
Get:53 http://deb.debian.org/debian unstable/main amd64 dh-python all 5.20221008 [115 kB]
Get:54 http://deb.debian.org/debian unstable/main amd64 dos2unix amd64 7.4.3-1 [430 kB]
Get:55 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.0.9-2+b4 [275 kB]
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Get:58 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.50.0-1+b1 [73.1 kB]
Get:59 http://deb.debian.org/debian unstable/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB]
Get:60 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB]
Get:61 http://deb.debian.org/debian unstable/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB]
Get:62 http://deb.debian.org/debian unstable/main amd64 libcurl3-gnutls amd64 7.85.0-1 [361 kB]
Get:63 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 7.85.0-1 [457 kB]
Get:64 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB]
Get:65 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB]
Get:66 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20221009-1 [92.6 kB]
Get:67 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.4.9-1 [156 kB]
Get:68 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB]
Get:69 http://deb.debian.org/debian unstable/main amd64 libhts3 amd64 1.16+ds-2 [433 kB]
Get:70 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.2.5-2.1 [229 kB]
Get:71 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-4.1 [193 kB]
Get:72 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.16+ds-2 [1605 kB]
Get:73 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:74 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-1 [119 kB]
Get:75 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 4.5.0-4 [142 kB]
Get:76 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.0-6 [36.3 kB]
Get:77 http://deb.debian.org/debian unstable/main amd64 libpython3.10 amd64 3.10.7-2 [1753 kB]
Get:78 http://deb.debian.org/debian unstable/main amd64 libpython3.10-dev amd64 3.10.7-2 [4121 kB]
Get:79 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.10.6-1 [22.0 kB]
Get:80 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.10.6-1 [1068 B]
Get:81 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B]
Get:82 http://deb.debian.org/debian unstable/main amd64 ruby3.0 amd64 3.0.4-8 [683 kB]
Get:83 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.3.15-1 [293 kB]
Get:84 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.0+3.1 [12.2 kB]
Get:85 http://deb.debian.org/debian unstable/main amd64 rake all 13.0.6-3 [83.9 kB]
Get:86 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.1.1-2.1 [12.7 kB]
Get:87 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.7.0-4 [50.9 kB]
Get:88 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB]
Get:89 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5 [18.5 kB]
Get:90 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB]
Get:91 http://deb.debian.org/debian unstable/main amd64 libruby3.0 amd64 3.0.4-8 [5399 kB]
Get:92 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.0+3.1 [11.3 kB]
Get:93 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.0-6 [29.8 kB]
Get:94 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.0-6 [26.1 kB]
Get:95 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.10.6-1 [1060 B]
Get:96 http://deb.debian.org/debian unstable/main amd64 python3.10-dev amd64 3.10.7-2 [508 kB]
Get:97 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.10.6-1 [25.4 kB]
Get:98 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.10.6-1 [1068 B]
Get:99 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.16.1-1 [607 kB]
Get:100 http://deb.debian.org/debian unstable/main amd64 swig4.0 amd64 4.0.2-2 [1386 kB]
Get:101 http://deb.debian.org/debian unstable/main amd64 swig all 4.0.2-2 [330 kB]
Get:102 http://deb.debian.org/debian unstable/main amd64 time amd64 1.9-0.2 [50.8 kB]
Get:103 http://deb.debian.org/debian unstable/main amd64 yaggo all 1.5.10-5 [21.4 kB]
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Adding 'diversion of /usr/bin/pkg-config to /usr/bin/pkg-config.real by pkgconf'
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up libcurl3-gnutls:amd64 (7.85.0-1) ...
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Setting up libpython3.10-stdlib:amd64 (3.10.7-2) ...
Setting up dh-autoreconf (20) ...
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Updating certificates in /etc/ssl/certs...
127 added, 0 removed; done.
Setting up libjs-sphinxdoc (4.5.0-4) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
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Setting up python3 (3.10.6-1) ...
Setting up rubygems-integration (1.18) ...
Setting up man-db (2.11.0-1+b1) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libpython3.10-dev:amd64 (3.10.7-2) ...
Setting up python3.10-dev (3.10.7-2) ...
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Setting up libpython3-all-dev:amd64 (3.10.6-1) ...
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Setting up rake (13.0.6-3) ...
Setting up ruby3.0 (3.0.4-8) ...
Setting up libruby3.0:amd64 (3.0.4-8) ...
Setting up libruby:amd64 (1:3.0+3.1) ...
Setting up ruby (1:3.0+3.1) ...
Setting up yaggo (1.5.10-5) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up ruby-sdbm:amd64 (1.0.0-5) ...
Setting up ruby-rubygems (3.3.15-1) ...
Processing triggers for libc-bin (2.35-3) ...
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 (amd64 included in amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64 all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 5.18.0-0.bpo.1-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 5.18.2-1~bpo11+1 (2022-06-14) amd64 (x86_64)
Toolchain package versions: binutils_2.39-8 dpkg-dev_1.21.9 g++-12_12.2.0-5 gcc-12_12.2.0-5 libc6-dev_2.35-3 libstdc++-12-dev_12.2.0-5 libstdc++6_12.2.0-5 linux-libc-dev_6.0.2-1
Package versions: adduser_3.129 apt_2.5.3+b1 autoconf_2.71-2 autoconf-archive_20220903-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.3 base-passwd_3.6.1 bash_5.2-1 bc_1.07.1-3+b1 binutils_2.39-8 binutils-common_2.39-8 binutils-x86-64-linux-gnu_2.39-8 bsdextrautils_2.38.1-1.1+b1 bsdutils_1:2.38.1-1.1+b1 build-essential_12.9 bzip2_1.0.8-5+b1 ca-certificates_20211016 ccache_4.7-1 chrpath_0.16-2+b1 coreutils_9.1-1 cpp_4:12.2.0-1 cpp-12_12.2.0-5 d-shlibs_0.104 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.10 debian-archive-keyring_2021.1.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-python_5.20221008 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1+b1 dos2unix_7.4.3-1 dpkg_1.21.9+b1 dpkg-dev_1.21.9 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1+b1 eatmydata_130-2 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1 g++-12_12.2.0-5 gcc_4:12.2.0-1 gcc-12_12.2.0-5 gcc-12-base_12.2.0-5 gettext_0.21-9 gettext-base_0.21-9 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1+b1 gpg_2.2.39-1+b1 gpg-agent_2.2.39-1+b1 gpg-wks-client_2.2.39-1+b1 gpg-wks-server_2.2.39-1+b1 gpgconf_2.2.39-1+b1 gpgsm_2.2.39-1+b1 gpgv_2.2.39-1+b1 grep_3.8-2 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-1 libapt-pkg6.0_2.5.3+b1 libarchive-zip-perl_1.68-1 libasan8_12.2.0-5 libassuan0_2.5.5-4 libatomic1_12.2.0-5 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1+b1 libbinutils_2.39-8 libblkid1_2.38.1-1.1+b1 libbrotli1_1.0.9-2+b4 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b1 libc-bin_2.35-3 libc-dev-bin_2.35-3 libc6_2.35-3 libc6-dev_2.35-3 libcap-ng0_0.8.3-1+b1 libcap2_1:2.44-1 libcc1-0_12.2.0-5 libcom-err2_1.46.6~rc1-1+b1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-8 libctf0_2.39-8 libcurl3-gnutls_7.85.0-1 libcurl4-gnutls-dev_7.85.0-1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.10 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdpkg-perl_1.21.9 libeatmydata1_130-2+b1 libedit2_3.1-20221009-1 libelf1_0.187-4 libexpat1_2.4.9-1 libexpat1-dev_2.4.9-1 libext2fs2_1.46.6~rc1-1+b1 libfakeroot_1.29-1 libffi8_3.4.3-2 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.2.0-5 libgcc-s1_12.2.0-5 libgcrypt20_1.10.1-2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-5 libgpg-error0_1.45-2 libgprofng0_2.39-8 libgssapi-krb5-2_1.20-1+b1 libhiredis0.14_0.14.1-3 libhogweed6_3.8.1-2 libhts-dev_1.16+ds-2 libhts3_1.16+ds-2 libhtscodecs2_1.3.0-4 libicu71_71.1-3 libidn2-0_2.3.3-1+b1 libisl23_0.25-1 libitm1_12.2.0-5 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_4.5.0-4 libjs-underscore_1.13.4~dfsg+~1.11.4-1 libk5crypto3_1.20-1+b1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1+b1 libkrb5support0_1.20-1+b1 libksba8_1.6.2-2 libldap-2.5-0_2.5.13+dfsg-2 liblsan0_12.2.0-5 liblz4-1_1.9.4-1 liblzma-dev_5.2.5-2.1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-1.1+b1 libmpc3_1.2.1-2 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.50.0-1+b1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpcre2-8-0_10.40-1 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.6-3 libpkgconf3_1.8.0-6 libprocps8_2:3.3.17-7+b1 libpsl5_0.21.0-1.2 libpython3-all-dev_3.10.6-1 libpython3-dev_3.10.6-1 libpython3-stdlib_3.10.6-1 libpython3.10_3.10.7-2 libpython3.10-dev_3.10.7-2 libpython3.10-minimal_3.10.7-2 libpython3.10-stdlib_3.10.7-2 libquadmath0_12.2.0-5 libreadline8_8.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libruby_1:3.0+3.1 libruby3.0_3.0.4-8 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+b1 libselinux1_3.4-1+b2 libsemanage-common_3.4-1 libsemanage2_3.4-1+b2 libsepol2_3.4-2 libsmartcols1_2.38.1-1.1+b1 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1+b1 libssh2-1_1.10.0-3+b1 libssl3_3.0.5-4 libstdc++-12-dev_12.2.0-5 libstdc++6_12.2.0-5 libsub-override-perl_0.09-4 libsystemd0_251.6-1 libtasn1-6_4.19.0-2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libtsan2_12.2.0-5 libubsan1_12.2.0-5 libuchardet0_0.0.7-1 libudev1_251.6-1 libunistring2_1.0-2 libuuid1_2.38.1-1.1+b1 libxml2_2.9.14+dfsg-1+b1 libxxhash0_0.8.1-1 libyaml-0-2_0.2.5-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_6.0.2-1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1+b1 lsb-base_11.4 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.0-1+b1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-1.1+b1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 openssl_3.0.5-4 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.1-1 pkgconf_1.8.0-6 pkgconf-bin_1.8.0-6 po-debconf_1.0.21+nmu1 procps_2:3.3.17-7+b1 python3_3.10.6-1 python3-all_3.10.6-1 python3-all-dev_3.10.6-1 python3-dev_3.10.6-1 python3-distutils_3.10.7-1 python3-lib2to3_3.10.7-1 python3-minimal_3.10.6-1 python3.10_3.10.7-2 python3.10-dev_3.10.7-2 python3.10-minimal_3.10.7-2 rake_13.0.6-3 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 ruby_1:3.0+3.1 ruby-net-telnet_0.1.1-2.1 ruby-rubygems_3.3.15-1 ruby-sdbm_1.0.0-5 ruby-webrick_1.7.0-4 ruby-xmlrpc_0.3.2-2 ruby3.0_3.0.4-8 rubygems-integration_1.18 samtools_1.16.1-1 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_3.05-6 tar_1.34+dfsg-1 time_1.9-0.2 tzdata_2022e-1 usr-is-merged_33 util-linux_2.38.1-1.1+b1 util-linux-extra_2.38.1-1.1+b1 xz-utils_5.2.5-2.1 yaggo_1.5.10-5 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| 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: 2.3.0-15
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Shaun Jackman <sjackman at debian.org>, Andreas Tille <tille at debian.org>, Michael R. Crusoe <crusoe at debian.org>, ?tienne Mollier <emollier at debian.org>
Homepage: https://github.com/gmarcais/Jellyfish
Standards-Version: 4.6.1
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, autoconf-archive, 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
dcb7d3cd40572c6cabf719addd384aa9c2f34c5d 15376 jellyfish_2.3.0-15.debian.tar.xz
Checksums-Sha256:
29ead991de90151dbe4a2717f7ac30b3852296c9cbdda8b001121a1f2fa714db 679125 jellyfish_2.3.0.orig.tar.gz
9c3b7bccfa8ba49078452b8bd6534295cfa1eb84bd4ab0c5b395b93fae8f8d7c 15376 jellyfish_2.3.0-15.debian.tar.xz
Files:
b447a26df0f1e11526129907a9b0acdb 679125 jellyfish_2.3.0.orig.tar.gz
0869f7bc0fe3da61452888ad0c293dd3 15376 jellyfish_2.3.0-15.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.8u7Zx0Qt/trustedkeys.kbx': General error
gpgv: Signature made Wed Sep 28 20:08:02 2022 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille at debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./jellyfish_2.3.0-15.dsc
dpkg-source: info: extracting jellyfish in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking jellyfish_2.3.0.orig.tar.gz
dpkg-source: info: unpacking jellyfish_2.3.0-15.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
dpkg-source: info: applying gcc-12.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ADDRESS=en_GB.UTF-8
LC_ALL=C.UTF-8
LC_IDENTIFICATION=en_GB.UTF-8
LC_MEASUREMENT=en_GB.UTF-8
LC_MONETARY=en_GB.UTF-8
LC_NAME=en_GB.UTF-8
LC_NUMERIC=en_GB.UTF-8
LC_PAPER=en_GB.UTF-8
LC_TELEPHONE=en_GB.UTF-8
LC_TIME=en_GB.UTF-8
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=0
SCHROOT_GROUP=root
SCHROOT_SESSION_ID=unstable-amd64-sbuild-ec7a321c-e863-4830-b3d0-41cf13e7abb2
SCHROOT_UID=0
SCHROOT_USER=root
SHELL=/bin/sh
USER=root
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -b -rfakeroot
dpkg-buildpackage: info: source package jellyfish
dpkg-buildpackage: info: source version 2.3.0-15
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
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
dh binary --with python3
debian/rules override_dh_update_autotools_config
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# use python configuration from autoconf-archive
mv m4/m4-ax_python_devel.m4 /tmp
dh_update_autotools_config
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:8: warning: The macro `AC_PROG_LIBTOOL' is obsolete.
configure.ac:8: You should run autoupdate.
m4/libtool.m4:100: 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=x86_64-linux-gnu --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/x86_64-linux-gnu --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... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
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
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checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
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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
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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
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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 x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
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checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking if gcc supports -fno-rtti -fno-exceptions... no
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checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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checking for ld... /usr/bin/ld -m elf_x86_64
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checking for shared library run path origin... done
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checking whether the compiler supports GNU C++... yes
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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 -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
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/bin/grep: warning: stray \ before -
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checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking 32-bit host C ABI... no
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checking whether AVX512-F is supported by the processor... no
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checking for sys/syscall.h... yes
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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 sysconfig Python package... yes
checking for Python include path... -I/usr/include/python3.10
checking for Python library path... -L/usr/lib/x86_64-linux-gnu -lpython3.10
checking for Python site-packages path... /usr/lib/python3.10/site-packages
checking for Python platform specific site-packages path... /usr/lib/python3.10/site-packages
checking python extra libraries... -lcrypt -ldl -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/x86_64-linux-gnu/perl/5.36/CORE
checking for Perl extension target directory... /usr/lib/perl/5.36.0
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=x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread"
-I/usr/include/jellyfish-2.3.0
-L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread
-L/usr/lib/x86_64-linux-gnu
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:240: python3.10 setup.py config
/<<PKGBUILDDIR>>/swig/python/setup.py:12: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
from distutils.core import setup, Extension
running config
mv /tmp/m4-ax_python_devel.m4 m4
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
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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_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
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
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/usr/lib/x86_64-linux-gnu -lhts -R/usr/lib/x86_64-linux-gnu -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/usr/lib/x86_64-linux-gnu -lhts -R/usr/lib/x86_64-linux-gnu -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 -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/usr/lib/x86_64-linux-gnu ./.libs/libgtest.a -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu
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/usr/lib/x86_64-linux-gnu -lhts -R/usr/lib/x86_64-linux-gnu -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 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/fastq2sam jellyfish/fastq2sam.o -L/usr/lib/x86_64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu
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dh_auto_install -- install-data
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no install-data
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/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu && { 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/x86_64-linux-gnu && { 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/x86_64-linux-gnu/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a
libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu'
/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/x86_64-linux-gnu'
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/5.36.0'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0'
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/5.36.0 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/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/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/5.36.0/jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0 && { 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/5.36.0 && { 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/5.36.0/jellyfish.la
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.36.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0'
/usr/bin/install -c swig/perl5/jellyfish.pm '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-2.0.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-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/python3.10/site-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/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/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/python3.10/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-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/python3.10/site-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/python3.10/site-packages/dna_jellyfish/_dna_jellyfish.la
libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/python3.10/site-packages/dna_jellyfish'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish'
/usr/bin/install -c swig/python/__init__.pyc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-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/x86_64-linux-gnu'
/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu && { 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/x86_64-linux-gnu && { 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/x86_64-linux-gnu/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a
libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0'
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/5.36.0 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/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/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/5.36.0/jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0 && { 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/5.36.0 && { 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/5.36.0/jellyfish.la
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.36.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0'
/usr/bin/install -c swig/perl5/jellyfish.pm '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.36.0'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-2.0.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-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/python3.10/site-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/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/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/python3.10/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-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/python3.10/site-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/python3.10/site-packages/dna_jellyfish/_dna_jellyfish.la
libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/python3.10/site-packages/dna_jellyfish'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish'
/usr/bin/install -c swig/python/__init__.pyc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.10/site-packages/dna_jellyfish'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build --sourcedirectory=swig/perl5
cd swig/perl5 && make -j3
make[2]: Entering directory '/<<PKGBUILDDIR>>/swig/perl5'
Running Mkbootstrap for jellyfish ()
chmod 644 "jellyfish.bs"
g++ -c -std=c++0x -I/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/x86_64-linux-gnu/perl/5.36/CORE" swig_wrap.cpp
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644
swig_wrap.cpp:1609:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory
1609 | #include <jellyfish/mer_dna.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [Makefile:342: swig_wrap.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/swig/perl5'
dh_auto_build: error: cd swig/perl5 && make -j3 returned exit code 2
make[1]: *** [debian/rules:87: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:22: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2022-10-19T15:17:59Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: amd64
Build Type: binary
Build-Space: 181608
Build-Time: 170
Distribution: unstable
Fail-Stage: build
Host Architecture: amd64
Install-Time: 53
Job: jellyfish
Machine Architecture: amd64
Package: jellyfish
Package-Time: 323
Source-Version: 2.3.0-15
Space: 181608
Status: attempted
Version: 2.3.0-15
--------------------------------------------------------------------------------
Finished at 2022-10-19T15:17:59Z
Build needed 00:05:23, 181608k disk space
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