sbuild (Debian sbuild) 0.85.11~bpo12+1 (31 August 2024) on debusine-worker-arm64-demeter-05.freexian.com
+==============================================================================+
| jellyfish 2.3.1-3+bd1 (arm64) Thu, 24 Oct 2024 05:15:16 +0000 |
+==============================================================================+
Package: jellyfish
Version: 2.3.1-3+bd1
Source Version: 2.3.1-3
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: any
I: No tarballs found in /var/lib/debusine/worker/.cache/sbuild
Unpacking /var/lib/debusine/worker/system-images/872923/system.tar.xz to /tmp/tmp.sbuild.AfJKsNrgVd...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'
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| Chroot Setup Commands |
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rm -f /etc/resolv.conf
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Copying /tmp/debusine-fetch-exec-upload-8aiaj_tc/libpython3-all-dbg_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
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Copying /tmp/debusine-fetch-exec-upload-8aiaj_tc/python3-all-dbg_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
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Copying /tmp/debusine-fetch-exec-upload-8aiaj_tc/python3-dev_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
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Copying /tmp/debusine-fetch-exec-upload-8aiaj_tc/python3-venv_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-8aiaj_tc/python3_3.12.6-1+debusine1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-8aiaj_tc/2to3_3.12.6-1+debusine1_all.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-8aiaj_tc/idle_3.12.6-1+debusine1_all.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-8aiaj_tc/python3-doc_3.12.6-1+debusine1_all.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-8aiaj_tc/python3-examples_3.12.6-1+debusine1_all.deb to /<<CHROOT>>...
I: NOTICE: Log filtering will replace 'build/jellyfish-uXFg6p/resolver-6yebj9' with '<<RESOLVERDIR>>'
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| Update chroot |
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Get:1 file:/build/jellyfish-uXFg6p/resolver-65kx59/apt_archive ./ InRelease
Ign:1 file:/build/jellyfish-uXFg6p/resolver-65kx59/apt_archive ./ InRelease
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Get:3 http://deb.debian.org/debian sid InRelease [202 kB]
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Get:4 file:/build/jellyfish-uXFg6p/resolver-65kx59/apt_archive ./ Release.gpg
Ign:4 file:/build/jellyfish-uXFg6p/resolver-65kx59/apt_archive ./ Release.gpg
Get:5 file:/build/jellyfish-uXFg6p/resolver-65kx59/apt_archive ./ Packages [20.5 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 Packages [9914 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 Components [4912 kB]
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Reading package lists...
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Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
apt base-passwd coreutils libapt-pkg6.0t64 libhtml-form-perl libkeyutils1
liblz1 libnet-ssleay-perl sysvinit-utils
9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 5601 kB of archives.
After this operation, 142 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main arm64 coreutils arm64 9.5-1 [2858 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 libapt-pkg6.0t64 arm64 2.9.10 [922 kB]
Get:3 http://deb.debian.org/debian sid/main arm64 base-passwd arm64 3.6.5 [52.8 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 apt arm64 2.9.10 [1332 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 sysvinit-utils arm64 3.11-1 [33.0 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 libhtml-form-perl all 6.12-1 [32.3 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 libkeyutils1 arm64 1.6.3-3.1 [9256 B]
Get:8 http://deb.debian.org/debian sid/main arm64 liblz1 arm64 1.15~pre2-1 [38.1 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 libnet-ssleay-perl arm64 1.94-2 [323 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libnet-ssleay-perl:arm64 (1.94-2) over (1.94-1+b2) ...
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Setting up libkeyutils1:arm64 (1.6.3-3.1) ...
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| Fetch source files |
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Local sources
-------------
/tmp/debusine-fetch-exec-upload-8aiaj_tc/jellyfish_2.3.1-3.dsc exists in /tmp/debusine-fetch-exec-upload-8aiaj_tc; copying to chroot
I: NOTICE: Log filtering will replace 'build/jellyfish-uXFg6p/jellyfish-2.3.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/jellyfish-uXFg6p' with '<<BUILDDIR>>'
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| Install package build dependencies |
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Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, architecture-is-64-bit, d-shlibs, autoconf-archive, yaggo, pkgconf, bc, time, procps, swig, python3-all-dev, dh-sequence-python3, python3-setuptools, perl, chrpath, libhts-dev, dos2unix, samtools, build-essential, fakeroot, dumb-init
Filtered Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, architecture-is-64-bit, d-shlibs, autoconf-archive, yaggo, pkgconf, bc, time, procps, swig, python3-all-dev, dh-sequence-python3, python3-setuptools, perl, chrpath, libhts-dev, dos2unix, samtools, build-essential, fakeroot, dumb-init
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
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Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [889 B]
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Reading package lists...
Get:1 file:/<<BUILDDIR>>/resolver-65kx59/apt_archive ./ InRelease
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Get:2 file:/<<BUILDDIR>>/resolver-65kx59/apt_archive ./ Release [609 B]
Get:2 file:/<<BUILDDIR>>/resolver-65kx59/apt_archive ./ Release [609 B]
Get:3 file:/<<BUILDDIR>>/resolver-65kx59/apt_archive ./ Release.gpg
Ign:3 file:/<<BUILDDIR>>/resolver-65kx59/apt_archive ./ Release.gpg
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
architecture-properties autoconf autoconf-archive automake autopoint
autotools-dev bc build-essential chrpath cpp cpp-14 cpp-14-aarch64-linux-gnu
cpp-aarch64-linux-gnu d-shlibs debhelper dh-autoreconf dh-python
dh-strip-nondeterminism dos2unix dumb-init dwz fakeroot g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libbrotli-dev
libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libedit2 libelf1t64
libevent-2.1-7t64 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev libgmpxx4ldbl
libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libhts-dev
libhts3t64 libhtscodecs2 libhwasan0 libidn2-dev libisl23 libitm1
libjs-jquery libjs-sphinxdoc libjs-underscore liblsan0 liblzma-dev libmpc3
libmpfr6 libncurses6 libncursesw6 libnghttp2-dev libnghttp3-dev
libngtcp2-crypto-gnutls-dev libngtcp2-dev libnsl2 libp11-kit-dev libpkgconf3
libproc2-0 libpsl-dev libpython3-all-dev libpython3-dev libpython3-stdlib
libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib
libpython3.12t64 libpython3.13 libpython3.13-dev libpython3.13-minimal
libpython3.13-stdlib librtmp-dev libruby libruby3.1t64 libssh2-1-dev
libssl-dev libstdc++-14-dev libtasn1-6-dev libtirpc-common libtirpc3t64
libtool libtsan2 libubsan1 libunbound8 libzstd-dev linux-libc-dev m4
media-types nettle-dev pkgconf pkgconf-bin po-debconf procps python3
python3-all python3-all-dev python3-autocommand python3-dev python3-inflect
python3-jaraco.context python3-jaraco.functools python3-minimal
python3-more-itertools python3-pkg-resources python3-setuptools
python3-typeguard python3-typing-extensions python3-zipp python3.12
python3.12-dev python3.12-minimal python3.13 python3.13-dev
python3.13-minimal rake rpcsvc-proto ruby ruby-net-telnet ruby-rubygems
ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools
swig time yaggo zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc cpp-doc gcc-14-locales cpp-14-doc dh-make flit
python3-build python3-installer python3-wheel gcc-14-doc gcc-multilib
manpages-dev flex bison gdb gcc-doc gdb-aarch64-linux-gnu libc-devtools
glibc-doc libcurl4-doc libidn-dev libkrb5-dev libldap2-dev gmp-doc
libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc liblzma-doc
libnghttp2-doc p11-kit-doc libssl-doc libstdc++-14-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc libmail-box-perl python3-doc python3-tk
python3-venv python-setuptools-doc python3.12-venv python3.12-doc
binfmt-support python3.13-venv python3.13-doc ri ruby-dev bundler cwltool
swig-doc swig-examples
Recommended packages:
manpages manpages-dev libarchive-cpio-perl javascript-common libgpm2
libtasn1-doc libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults
zip fonts-lato
The following NEW packages will be installed:
architecture-properties autoconf autoconf-archive automake autopoint
autotools-dev bc build-essential chrpath cpp cpp-14 cpp-14-aarch64-linux-gnu
cpp-aarch64-linux-gnu d-shlibs debhelper dh-autoreconf dh-python
dh-strip-nondeterminism dos2unix dumb-init dwz fakeroot g++ g++-14
g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libbrotli-dev
libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libedit2 libelf1t64
libevent-2.1-7t64 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev libgmpxx4ldbl
libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libhts-dev
libhts3t64 libhtscodecs2 libhwasan0 libidn2-dev libisl23 libitm1
libjs-jquery libjs-sphinxdoc libjs-underscore liblsan0 liblzma-dev libmpc3
libmpfr6 libncurses6 libncursesw6 libnghttp2-dev libnghttp3-dev
libngtcp2-crypto-gnutls-dev libngtcp2-dev libnsl2 libp11-kit-dev libpkgconf3
libproc2-0 libpsl-dev libpython3-all-dev libpython3-dev libpython3-stdlib
libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib
libpython3.12t64 libpython3.13 libpython3.13-dev libpython3.13-minimal
libpython3.13-stdlib librtmp-dev libruby libruby3.1t64 libssh2-1-dev
libssl-dev libstdc++-14-dev libtasn1-6-dev libtirpc-common libtirpc3t64
libtool libtsan2 libubsan1 libunbound8 libzstd-dev linux-libc-dev m4
media-types nettle-dev pkgconf pkgconf-bin po-debconf procps python3
python3-all python3-all-dev python3-autocommand python3-dev python3-inflect
python3-jaraco.context python3-jaraco.functools python3-minimal
python3-more-itertools python3-pkg-resources python3-setuptools
python3-typeguard python3-typing-extensions python3-zipp python3.12
python3.12-dev python3.12-minimal python3.13 python3.13-dev
python3.13-minimal rake rpcsvc-proto ruby ruby-net-telnet ruby-rubygems
ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools
sbuild-build-depends-main-dummy swig time yaggo zlib1g-dev
0 upgraded, 148 newly installed, 0 to remove and 0 not upgraded.
Need to get 114 MB/114 MB of archives.
After this operation, 471 MB of additional disk space will be used.
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Get:2 file:/<<BUILDDIR>>/resolver-65kx59/apt_archive ./ python3-minimal 3.12.6-1+debusine1 [26.8 kB]
Get:3 file:/<<BUILDDIR>>/resolver-65kx59/apt_archive ./ libpython3-stdlib 3.12.6-1+debusine1 [9732 B]
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Get:7 file:/<<BUILDDIR>>/resolver-65kx59/apt_archive ./ python3-all 3.12.6-1+debusine1 [1056 B]
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Get:9 file:/<<BUILDDIR>>/resolver-65kx59/apt_archive ./ python3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:10 http://deb.debian.org/debian sid/main arm64 autoconf-archive all 20220903-3 [775 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.7-1 [807 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 python3.12-minimal arm64 3.12.7-1 [1941 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 libncursesw6 arm64 6.5-2 [124 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 libpython3.12-stdlib arm64 3.12.7-1 [1901 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 python3.12 arm64 3.12.7-1 [671 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libpython3.13-minimal arm64 3.13.0-1 [849 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 python3.13-minimal arm64 3.13.0-1 [1835 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 procps arm64 2:4.0.4-6 [872 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 architecture-properties arm64 0.2.3 [2184 B]
Get:26 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 bc arm64 1.07.1-4 [101 kB]
Get:32 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.4-1 [2440 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 rpcsvc-proto arm64 1.4.3-1 [59.7 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 libisl23 arm64 0.27-1 [601 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 libmpfr6 arm64 4.2.1-1+b1 [674 kB]
Get:39 http://deb.debian.org/debian sid/main arm64 libmpc3 arm64 1.3.1-1+b2 [50.2 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-7 [9164 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 cpp-14 arm64 14.2.0-7 [1280 B]
Get:42 http://deb.debian.org/debian sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1 [4832 B]
Get:43 http://deb.debian.org/debian sid/main arm64 cpp arm64 4:14.2.0-1 [1568 B]
Get:44 http://deb.debian.org/debian sid/main arm64 libcc1-0 arm64 14.2.0-7 [42.2 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-7 [24.2 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-7 [2578 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-7 [1162 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-7 [2386 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-7 [1040 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-7 [1442 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-7 [2365 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-7 [17.7 MB]
Get:53 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-7 [517 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1 [1440 B]
Get:55 http://deb.debian.org/debian sid/main arm64 gcc arm64 4:14.2.0-1 [5136 B]
Get:56 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-7 [2265 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-7 [10.1 MB]
Get:58 http://deb.debian.org/debian sid/main arm64 g++-14 arm64 14.2.0-7 [20.0 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1 [1200 B]
Get:60 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B]
Get:61 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:62 http://deb.debian.org/debian sid/main arm64 chrpath arm64 0.16-2+b1 [16.0 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 d-shlibs all 0.107 [11.0 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-7 [517 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:69 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:76 http://deb.debian.org/debian sid/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB]
Get:77 http://deb.debian.org/debian sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:78 http://deb.debian.org/debian sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:79 http://deb.debian.org/debian sid/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB]
Get:81 http://deb.debian.org/debian sid/main arm64 python3-zipp all 3.20.2-1 [10.3 kB]
Get:82 http://deb.debian.org/debian sid/main arm64 python3-setuptools all 74.1.2-2 [736 kB]
Get:83 http://deb.debian.org/debian sid/main arm64 dh-python all 6.20240824 [109 kB]
Get:84 http://deb.debian.org/debian sid/main arm64 dos2unix arm64 7.5.2-1 [515 kB]
Get:85 http://deb.debian.org/debian sid/main arm64 dumb-init arm64 1.2.5-3 [13.4 kB]
Get:86 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:87 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:88 http://deb.debian.org/debian sid/main arm64 libbrotli-dev arm64 1.1.0-2+b4 [308 kB]
Get:89 http://deb.debian.org/debian sid/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10 [169 kB]
Get:90 http://deb.debian.org/debian sid/main arm64 libunbound8 arm64 1.22.0-1 [553 kB]
Get:91 http://deb.debian.org/debian sid/main arm64 libgnutls-dane0t64 arm64 3.8.6-2 [436 kB]
Get:92 http://deb.debian.org/debian sid/main arm64 libgnutls-openssl27t64 arm64 3.8.6-2 [436 kB]
Get:93 http://deb.debian.org/debian sid/main arm64 libidn2-dev arm64 2.3.7-2 [122 kB]
Get:94 http://deb.debian.org/debian sid/main arm64 libp11-kit-dev arm64 0.25.5-2 [208 kB]
Get:95 http://deb.debian.org/debian sid/main arm64 libtasn1-6-dev arm64 4.19.0-3+b2 [96.2 kB]
Get:96 http://deb.debian.org/debian sid/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b1 [329 kB]
Get:97 http://deb.debian.org/debian sid/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b1 [619 kB]
Get:98 http://deb.debian.org/debian sid/main arm64 nettle-dev arm64 3.10-1 [1323 kB]
Get:99 http://deb.debian.org/debian sid/main arm64 libgnutls28-dev arm64 3.8.6-2 [1394 kB]
Get:100 http://deb.debian.org/debian sid/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get:101 http://deb.debian.org/debian sid/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get:102 http://deb.debian.org/debian sid/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
Get:103 http://deb.debian.org/debian sid/main arm64 libnghttp2-dev arm64 1.63.0-1 [112 kB]
Get:104 http://deb.debian.org/debian sid/main arm64 libnghttp3-dev arm64 1.4.0-1 [85.3 kB]
Get:105 http://deb.debian.org/debian sid/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.6.0-1 [23.7 kB]
Get:106 http://deb.debian.org/debian sid/main arm64 libngtcp2-dev arm64 1.6.0-1 [165 kB]
Get:107 http://deb.debian.org/debian sid/main arm64 libpsl-dev arm64 0.21.2-1.1 [77.7 kB]
Get:108 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB]
Get:109 http://deb.debian.org/debian sid/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b4 [67.3 kB]
Get:110 http://deb.debian.org/debian sid/main arm64 libssl-dev arm64 3.3.2-1 [3185 kB]
Get:111 http://deb.debian.org/debian sid/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB]
Get:112 http://deb.debian.org/debian sid/main arm64 libzstd-dev arm64 1.5.6+dfsg-1 [330 kB]
Get:113 http://deb.debian.org/debian sid/main arm64 libcurl4-gnutls-dev arm64 8.10.1-2 [456 kB]
Get:114 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get:115 http://deb.debian.org/debian sid/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB]
Get:116 http://deb.debian.org/debian sid/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB]
Get:117 http://deb.debian.org/debian sid/main arm64 libexpat1-dev arm64 2.6.3-1 [142 kB]
Get:118 http://deb.debian.org/debian sid/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB]
Get:119 http://deb.debian.org/debian sid/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB]
Get:120 http://deb.debian.org/debian sid/main arm64 liblzma-dev arm64 5.6.2-2 [296 kB]
Get:121 http://deb.debian.org/debian sid/main arm64 libhts-dev arm64 1.20+ds-1 [1613 kB]
Get:122 http://deb.debian.org/debian sid/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:123 http://deb.debian.org/debian sid/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:124 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 7.4.7-3 [158 kB]
Get:125 http://deb.debian.org/debian sid/main arm64 libncurses6 arm64 6.5-2 [95.7 kB]
Get:126 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.7-1 [1982 kB]
Get:127 http://deb.debian.org/debian sid/main arm64 libpython3.12-dev arm64 3.12.7-1 [4793 kB]
Get:128 http://deb.debian.org/debian sid/main arm64 libpython3.13-stdlib arm64 3.13.0-1 [1920 kB]
Get:129 http://deb.debian.org/debian sid/main arm64 libpython3.13 arm64 3.13.0-1 [1960 kB]
Get:130 http://deb.debian.org/debian sid/main arm64 libpython3.13-dev arm64 3.13.0-1 [4668 kB]
Get:131 http://deb.debian.org/debian sid/main arm64 rubygems-integration all 1.18 [6704 B]
Get:132 http://deb.debian.org/debian sid/main arm64 ruby3.1 arm64 3.1.2-8.4 [664 kB]
Get:133 http://deb.debian.org/debian sid/main arm64 ruby-rubygems all 3.4.20-1 [309 kB]
Get:134 http://deb.debian.org/debian sid/main arm64 ruby arm64 1:3.1+nmu1 [5584 B]
Get:135 http://deb.debian.org/debian sid/main arm64 rake all 13.2.1-1 [65.2 kB]
Get:136 http://deb.debian.org/debian sid/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB]
Get:137 http://deb.debian.org/debian sid/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB]
Get:138 http://deb.debian.org/debian sid/main arm64 ruby-xmlrpc all 0.3.3-2 [24.4 kB]
Get:139 http://deb.debian.org/debian sid/main arm64 ruby-sdbm arm64 1.0.0-5+b4 [14.6 kB]
Get:140 http://deb.debian.org/debian sid/main arm64 libruby3.1t64 arm64 3.1.2-8.4 [5266 kB]
Get:141 http://deb.debian.org/debian sid/main arm64 libruby arm64 1:3.1+nmu1 [4664 B]
Get:142 http://deb.debian.org/debian sid/main arm64 python3.13 arm64 3.13.0-1 [730 kB]
Get:143 http://deb.debian.org/debian sid/main arm64 python3.12-dev arm64 3.12.7-1 [505 kB]
Get:144 http://deb.debian.org/debian sid/main arm64 python3.13-dev arm64 3.13.0-1 [504 kB]
Get:145 http://deb.debian.org/debian sid/main arm64 samtools arm64 1.20-3 [624 kB]
Get:146 http://deb.debian.org/debian sid/main arm64 swig arm64 4.2.1-1 [1350 kB]
Get:147 http://deb.debian.org/debian sid/main arm64 time arm64 1.9-0.2 [50.6 kB]
Get:148 http://deb.debian.org/debian sid/main arm64 yaggo all 1.5.11-1 [21.3 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libpython3.12-minimal:arm64 (3.12.7-1) ...
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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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Setting up python3-minimal (3.12.6-1+debusine1) ...
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Setting up libasan8:arm64 (14.2.0-7) ...
Setting up procps (2:4.0.4-6) ...
Setting up libhts3t64:arm64 (1.20+ds-1) ...
Setting up python3.13-minimal (3.13.0-1) ...
Setting up dos2unix (7.5.2-1) ...
Setting up libtsan2:arm64 (14.2.0-7) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libisl23:arm64 (0.27-1) ...
Setting up libc-dev-bin (2.40-3) ...
Setting up libtasn1-6-dev:arm64 (4.19.0-3+b2) ...
Setting up libdeflate-dev:arm64 (1.22-1) ...
Setting up libpython3.13-stdlib:arm64 (3.13.0-1) ...
Setting up ruby-xmlrpc (0.3.3-2) ...
Setting up libcc1-0:arm64 (14.2.0-7) ...
Setting up libbrotli-dev:arm64 (1.1.0-2+b4) ...
Setting up chrpath (0.16-2+b1) ...
Setting up liblsan0:arm64 (14.2.0-7) ...
Setting up libp11-kit-dev:arm64 (0.25.5-2) ...
Setting up libitm1:arm64 (14.2.0-7) ...
Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Setting up libpython3.13:arm64 (3.13.0-1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-2+b1) ...
Setting up nettle-dev:arm64 (3.10-1) ...
Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ...
Setting up python3.13 (3.13.0-1) ...
Setting up pkgconf:arm64 (1.8.1-4) ...
Setting up samtools (1.20-3) ...
Setting up libjs-sphinxdoc (7.4.7-3) ...
Setting up cpp-14-aarch64-linux-gnu (14.2.0-7) ...
Setting up libnsl2:arm64 (1.3.0-3+b2) ...
Setting up libc6-dev:arm64 (2.40-3) ...
Setting up libgcc-14-dev:arm64 (14.2.0-7) ...
Setting up libstdc++-14-dev:arm64 (14.2.0-7) ...
Setting up libgnutls28-dev:arm64 (3.8.6-2) ...
Setting up libnghttp2-dev:arm64 (1.63.0-1) ...
Setting up libpython3.12-stdlib:arm64 (3.12.7-1) ...
Setting up python3.12 (3.12.7-1) ...
Setting up libpython3.12t64:arm64 (3.12.7-1) ...
Setting up cpp-aarch64-linux-gnu (4:14.2.0-1) ...
Setting up libexpat1-dev:arm64 (2.6.3-1) ...
Setting up cpp-14 (14.2.0-7) ...
Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ...
Setting up cpp (4:14.2.0-1) ...
Setting up gcc-14-aarch64-linux-gnu (14.2.0-7) ...
Setting up libpython3-stdlib:arm64 (3.12.6-1+debusine1) ...
Setting up gcc-aarch64-linux-gnu (4:14.2.0-1) ...
Setting up g++-14-aarch64-linux-gnu (14.2.0-7) ...
Setting up python3 (3.12.6-1+debusine1) ...
Setting up libpython3.12-dev:arm64 (3.12.7-1) ...
Setting up python3-zipp (3.20.2-1) ...
Setting up python3-autocommand (2.2.2-3) ...
Setting up gcc-14 (14.2.0-7) ...
Setting up libpython3.13-dev:arm64 (3.13.0-1) ...
Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ...
Setting up python3.12-dev (3.12.7-1) ...
Setting up python3-typing-extensions (4.12.2-2) ...
Setting up libssh2-1-dev:arm64 (1.11.1-1) ...
Setting up g++-aarch64-linux-gnu (4:14.2.0-1) ...
Setting up g++-14 (14.2.0-7) ...
Setting up python3-more-itertools (10.5.0-1) ...
Setting up libpython3-dev:arm64 (3.12.6-1+debusine1) ...
Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up python3-jaraco.context (6.0.0-1) ...
Setting up libtool (2.4.7-7) ...
Setting up python3.13-dev (3.13.0-1) ...
Setting up python3-typeguard (4.3.0-1) ...
Setting up python3-all (3.12.6-1+debusine1) ...
Setting up libcurl4-gnutls-dev:arm64 (8.10.1-2) ...
Setting up gcc (4:14.2.0-1) ...
Setting up dh-autoreconf (20) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up libpython3-all-dev:arm64 (3.12.6-1+debusine1) ...
Setting up python3-dev (3.12.6-1+debusine1) ...
Setting up g++ (4:14.2.0-1) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up build-essential (12.12) ...
Setting up python3-pkg-resources (74.1.2-2) ...
Setting up python3-all-dev (3.12.6-1+debusine1) ...
Setting up python3-setuptools (74.1.2-2) ...
Setting up libhts-dev:arm64 (1.20+ds-1) ...
Setting up debhelper (13.20) ...
Setting up dh-python (6.20240824) ...
Setting up rake (13.2.1-1) ...
Setting up ruby-sdbm:arm64 (1.0.0-5+b4) ...
Setting up ruby-rubygems (3.4.20-1) ...
Setting up libruby3.1t64:arm64 (3.1.2-8.4) ...
Setting up ruby3.1 (3.1.2-8.4) ...
Setting up libruby:arm64 (1:3.1+nmu1) ...
Setting up ruby (1:3.1+nmu1) ...
Setting up yaggo (1.5.11-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.40-3) ...
Processing triggers for man-db (2.13.0-1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (arm64 included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) arm64 (aarch64)
Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.11 g++-14_14.2.0-7 gcc-14_14.2.0-7 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-7 libstdc++6_14.2.0-7 linux-libc-dev_6.11.4-1
Package versions: appstream_1.0.3-1 apt_2.9.10 architecture-properties_0.2.3 autoconf_2.72-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.5 bash_5.2.32-1+b2 bc_1.07.1-4 binutils_2.43.1-5 binutils-aarch64-linux-gnu_2.43.1-5 binutils-common_2.43.1-5 bsdextrautils_2.40.2-9 bsdutils_1:2.40.2-9 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20240203 chrpath_0.16-2+b1 coreutils_9.5-1 cpp_4:14.2.0-1 cpp-14_14.2.0-7 cpp-14-aarch64-linux-gnu_14.2.0-7 cpp-aarch64-linux-gnu_4:14.2.0-1 d-shlibs_0.107 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-python_6.20240824 dh-strip-nondeterminism_1.14.0-1 diffstat_1.66-1 diffutils_1:3.10-1 dos2unix_7.5.2-1 dpkg_1.22.11 dpkg-dev_1.22.11 dumb-init_1.2.5-3 dwz_0.15-1+b1 e2fsprogs_1.47.1-1 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-7 g++-14-aarch64-linux-gnu_14.2.0-7 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rake_13.2.1-1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 ruby_1:3.1+nmu1 ruby-net-telnet_0.2.0-1 ruby-rubygems_3.4.20-1 ruby-sdbm_1.0.0-5+b4 ruby-webrick_1.8.1-1 ruby-xmlrpc_0.3.3-2 ruby3.1_3.1.2-8.4 rubygems-integration_1.18 samtools_1.20-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 shared-mime-info_2.4-5+b1 swig_4.2.1-1 sysvinit-utils_3.11-1 t1utils_1.41-4 tar_1.35+dfsg-3 time_1.9-0.2 tzdata_2024b-3 ucf_3.0043+nmu1 unzip_6.0-28 util-linux_2.40.2-9 xz-utils_5.6.2-2 yaggo_1.5.11-1 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1
+------------------------------------------------------------------------------+
| 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: any all
Version: 2.3.1-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Shaun Jackman <sjackman@debian.org>, Andreas Tille <tille@debian.org>, Michael R. Crusoe <crusoe@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://www.genome.umd.edu/jellyfish.html
Standards-Version: 4.6.2
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), architecture-is-little-endian, architecture-is-64-bit, d-shlibs, autoconf-archive, yaggo, pkgconf, bc, time, procps, swig, python3-all-dev, dh-sequence-python3, python3-setuptools, perl, chrpath, libhts-dev, dos2unix, samtools
Package-List:
jellyfish deb science optional arch=any
jellyfish-examples deb science optional arch=all
libjellyfish-2.0-2 deb libs optional arch=any
libjellyfish-2.0-dev deb libdevel optional arch=any
libjellyfish-perl deb perl optional arch=any
python3-dna-jellyfish deb python optional arch=any
Checksums-Sha1:
9aaf5f07cecf638544d27ca3de7cb7057184c92c 681990 jellyfish_2.3.1.orig.tar.gz
32f49f1dd8cebe75a863a9b20b29e4a41223e1cc 13340 jellyfish_2.3.1-3.debian.tar.xz
Checksums-Sha256:
540d09457fb4e14b98c7f1428cf885c333e2d6ef4f6a3735aa06be13eb523d69 681990 jellyfish_2.3.1.orig.tar.gz
476e52f24cf5f7ac0bc1b047372d16fcbbc057e71ce5a5098c93d8726a9154b5 13340 jellyfish_2.3.1-3.debian.tar.xz
Files:
27fb29ad3edfe25d776cfbf98dcc8c0e 681990 jellyfish_2.3.1.orig.tar.gz
c7928f076800e7bc8f60f2ff07c5ce31 13340 jellyfish_2.3.1-3.debian.tar.xz
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gpgv: Signature made Tue Mar 19 17:22:40 2024 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./jellyfish_2.3.1-3.dsc: no acceptable signature found
dpkg-source: info: extracting jellyfish in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking jellyfish_2.3.1.orig.tar.gz
dpkg-source: info: unpacking jellyfish_2.3.1-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying drop_distutils
dpkg-source: info: applying manpage_whatis_entry.patch
dpkg-source: info: applying portability.patch
dpkg-source: info: applying test_needs_bash
dpkg-source: info: applying python3
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.3.1-3+bd1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=debusine-worker
OLDPWD=/
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SHELL=/bin/sh
USER=debusine-worker
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mDebusine Rebuild <debusine@example.net> -B -rfakeroot
dpkg-buildpackage: info: source package jellyfish
dpkg-buildpackage: info: source version 2.3.1-3+bd1
dpkg-buildpackage: info: source distribution sid
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
dh_clean
debian/rules execute_after_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
if [ -d debian/tmp_save_tests ] ; then \
mv debian/tmp_save_tests/* tests ; \
rmdir debian/tmp_save_tests ; \
fi
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules binary-arch
dh binary-arch
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 -a
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:8: 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=aarch64-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/aarch64-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... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-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... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether 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... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for ld... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for shared library run path origin... done
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking 32-bit host C ABI... no
checking for egrep -e... (cached) /usr/bin/grep -E
checking for ELF binary format... yes
checking for the common suffixes of directories in the library search path... lib,lib,lib
checking for htslib... yes
checking for samtools... /usr/bin/samtools
checking for unix2dos... /usr/bin/unix2dos
checking for md5sum... md5sum
checking for yaggo... /usr/bin/yaggo
checking for x86 cpuid output... unknown
checking for x86-AVX xgetbv output... unknown
checking for __int128... yes
checking for std::numeric_limits<__int128>... yes
checking for _NSGetExecutablePath... no
checking for execinfo.h... yes
checking for ext/stdio_filebuf.h... yes
checking for sys/syscall.h... yes
checking for sys/prctl.h... yes
checking for siginfo_t.si_int... yes
checking for swig... /usr/bin/swig
checking SWIG version... 4.2.1
checking for SWIG library... /usr/share/swig/4.2.1
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/python3.12
checking for Python library path... -L/usr/lib/aarch64-linux-gnu -lpython3.12
checking for Python site-packages path... /usr/lib/python3.12/site-packages
checking for Python platform specific site-packages path... /usr/lib/python3.12/site-packages
checking python extra libraries... -ldl -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/aarch64-linux-gnu/perl/5.40/CORE
checking for Perl extension target directory... /usr/lib/perl/5.40.0
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 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -lpthread"
-I/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.1
-L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -lpthread
-L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-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:311: python3.13 setup.py config
running config
I: pybuild base:311: python3.12 setup.py config
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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o jellyfish/merge_files.o jellyfish/merge_files.cc
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g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c unit_tests/gtest/src/gtest-all.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -pthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-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++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -pthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-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++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu ./.libs/libgtest.a -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o jellyfish/fastq2sam.o jellyfish/fastq2sam.cc
/bin/bash ./libtool --tag=CXX --mode=link g++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -pthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/fastq2sam jellyfish/fastq2sam.o libjellyfish-2.0.la
libtool: link: g++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/fastq2sam jellyfish/fastq2sam.o -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_install -- install-data
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no install-data
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make install-am
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu'
/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu'
/usr/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/aarch64-linux-gnu'
libtool: install: /usr/bin/install -c bin/.libs/jellyfish /<<PKGBUILDDIR>>/debian/tmp/usr/bin/jellyfish
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.1/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-2.3.1/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-2.3.1/jellyfish'
/usr/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'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
libtool: warning: relinking 'swig/perl5/jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -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/5.40.0/jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0 && { 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/5.40.0 && { 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/5.40.0/jellyfish.la
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/usr/bin/install -c swig/perl5/jellyfish.pm '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-2.0.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/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++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -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/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/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/python3.12/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/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la
libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
/usr/bin/install -c swig/python/__init__.pyc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.1/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-2.3.1/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-2.3.1/jellyfish'
/usr/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'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu'
/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
libtool: warning: relinking 'swig/perl5/jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -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/5.40.0/jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0 && { 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/5.40.0 && { 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/5.40.0/jellyfish.la
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/usr/bin/install -c swig/perl5/jellyfish.pm '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-2.0.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/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++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -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/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/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/python3.12/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/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la
libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
/usr/bin/install -c swig/python/__init__.pyc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build --sourcedirectory=swig/perl5
cd swig/perl5 && make -j8
make[2]: Entering directory '/<<PKGBUILDDIR>>/swig/perl5'
Running Mkbootstrap for jellyfish ()
g++ -c -std=c++0x -I/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.0.1\" -DXS_VERSION=\"0.0.1\" -fPIC "-I/usr/lib/aarch64-linux-gnu/perl/5.40/CORE" swig_wrap.cpp
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
chmod 644 "jellyfish.bs"
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644
rm -f blib/arch/auto/jellyfish/jellyfish.so
aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -lpthread -shared -L/usr/local/lib -fstack-protector-strong swig_wrap.o -o blib/arch/auto/jellyfish/jellyfish.so \
-lpthread \
chmod 755 blib/arch/auto/jellyfish/jellyfish.so
make[2]: Leaving directory '/<<PKGBUILDDIR>>/swig/perl5'
dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3.13 setup.py build build_ext -L/<<PKGBUILDDIR>>/.libs
running build
running build_py
copying dna_jellyfish.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dna_jellyfish/build
running build_ext
building '_dna_jellyfish' extension
creating build
creating build/temp.linux-aarch64-cpython-313
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.1 -I/usr/include/python3.13 -c swig_wrap.cpp -o build/temp.linux-aarch64-cpython-313/swig_wrap.o -std=c++0x
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/swig_wrap.o -L-L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -L/<<PKGBUILDDIR>>/.libs -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -lpthread -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dna_jellyfish/build/_dna_jellyfish.cpython-313-aarch64-linux-gnu.so -Wl,-rpath,-L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu
I: pybuild base:311: /usr/bin/python3 setup.py build build_ext -L/<<PKGBUILDDIR>>/.libs
running build
running build_py
copying dna_jellyfish.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_dna_jellyfish/build
running build_ext
building '_dna_jellyfish' extension
creating build/temp.linux-aarch64-cpython-312
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.1 -I/usr/include/python3.12 -c swig_wrap.cpp -o build/temp.linux-aarch64-cpython-312/swig_wrap.o -std=c++0x
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/swig_wrap.o -L-L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -L/<<PKGBUILDDIR>>/.libs -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -lpthread -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_dna_jellyfish/build/_dna_jellyfish.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,-L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
if ! dh_auto_test \
; then echo "E: tests failed, ./test-suite.log follows:" \
; cat ./test-suite.log \
; echo "E: end of ./test-suite.log after test failure." \
; exit 1 \
; fi
make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make check-am
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make bin/generate_sequence bin/fastq2sam bin/test_all libgtest.la libgtest_main.la
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: 'bin/generate_sequence' is up to date.
make[4]: 'bin/fastq2sam' is up to date.
make[4]: 'bin/test_all' is up to date.
make[4]: 'libgtest.la' is up to date.
/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 -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c -o unit_tests/gtest/src/libgtest_main_la-gtest_main.lo `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -o unit_tests/gtest/src/libgtest_main_la-gtest_main.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -pthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest_main.la unit_tests/gtest/src/libgtest_main_la-gtest_main.lo libgtest.la
libtool: link: (cd .libs/libgtest_main.lax/libgtest.a && ar x "/<<PKGBUILDDIR>>/./.libs/libgtest.a")
libtool: link: ar cr .libs/libgtest_main.a unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o .libs/libgtest_main.lax/libgtest.a/libgtest_la-gtest-all.o
libtool: link: ranlib .libs/libgtest_main.a
libtool: link: rm -fr .libs/libgtest_main.lax
libtool: link: ( cd ".libs" && rm -f "libgtest_main.la" && ln -s "../libgtest_main.la" "libgtest_main.la" )
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make check-TESTS
make[4]: Entering directory '/<<PKGBUILDDIR>>'
make[5]: Entering directory '/<<PKGBUILDDIR>>'
SKIP: tests/big.sh
PASS: tests/generate_sequence.sh
PASS: tests/subset_hashing.sh
PASS: tests/bloom_filter.sh
PASS: tests/bloom_counter.sh
PASS: tests/multi_file.sh
SKIP: tests/swig_ruby.sh
PASS: tests/swig_perl.sh
PASS: tests/sam.sh
PASS: tests/swig_python.sh
PASS: tests/large_key.sh
PASS: tests/merge.sh
PASS: tests/small_mers.sh
PASS: tests/parallel_hashing.sh
PASS: unit_tests/unit_tests.sh
============================================================================
Testsuite summary for jellyfish 2.3.1
============================================================================
# TOTAL: 15
# PASS: 13
# SKIP: 2
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[5]: Leaving directory '/<<PKGBUILDDIR>>'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
chrpath --delete bin/.libs/*
dh_auto_install -- install-data
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no install-data
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make install-am
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[4]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu'
/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu'
/usr/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/aarch64-linux-gnu'
libtool: install: /usr/bin/install -c bin/.libs/jellyfish /<<PKGBUILDDIR>>/debian/tmp/usr/bin/jellyfish
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.1/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-2.3.1/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-2.3.1/jellyfish'
/usr/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'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
libtool: warning: relinking 'swig/perl5/jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -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/5.40.0/jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0 && { 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/5.40.0 && { 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/5.40.0/jellyfish.la
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/usr/bin/install -c swig/perl5/jellyfish.pm '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-2.0.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/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++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -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/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/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/python3.12/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/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la
libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
/usr/bin/install -c swig/python/__init__.pyc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
make[4]: Leaving directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-2.3.1/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-2.3.1/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-2.3.1/jellyfish'
/usr/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'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu'
/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
libtool: warning: relinking 'swig/perl5/jellyfish.la'
libtool: install: (cd /<<PKGBUILDDIR>>; /bin/bash "/<<PKGBUILDDIR>>/libtool" --tag CXX --mode=relink g++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.40.0 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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -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/5.40.0/jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0 && { 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/5.40.0 && { 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/5.40.0/jellyfish.la
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0/jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.40.0'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/usr/bin/install -c swig/perl5/jellyfish.pm '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/perl/5.40.0'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-2.0.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
/bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/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++ -I/<<PKGBUILDDIR>>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -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/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/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/python3.12/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/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la
libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a
libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish'
/usr/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
/usr/bin/install -c swig/python/__init__.pyc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
running build
running build_py
copying dna_jellyfish.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dna_jellyfish/build
running build_ext
running install_lib
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.13
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dna_jellyfish/build/_dna_jellyfish.cpython-313-aarch64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dna_jellyfish/build/dna_jellyfish.py -> /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages
byte-compiling /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-313.pyc
running install_egg_info
running egg_info
creating dna_jellyfish.egg-info
writing dna_jellyfish.egg-info/PKG-INFO
writing dependency_links to dna_jellyfish.egg-info/dependency_links.txt
writing top-level names to dna_jellyfish.egg-info/top_level.txt
writing manifest file 'dna_jellyfish.egg-info/SOURCES.txt'
reading manifest file 'dna_jellyfish.egg-info/SOURCES.txt'
writing manifest file 'dna_jellyfish.egg-info/SOURCES.txt'
Copying dna_jellyfish.egg-info to /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.13/dist-packages/dna_jellyfish-0.0.1.egg-info
Skipping SOURCES.txt
running install_scripts
I: pybuild base:311: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
running build
running build_py
copying dna_jellyfish.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_dna_jellyfish/build
running build_ext
running install_lib
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.12
creating /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_dna_jellyfish/build/_dna_jellyfish.cpython-312-aarch64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_dna_jellyfish/build/dna_jellyfish.py -> /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages
byte-compiling /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-312.pyc
running install_egg_info
running egg_info
writing dna_jellyfish.egg-info/PKG-INFO
writing dependency_links to dna_jellyfish.egg-info/dependency_links.txt
writing top-level names to dna_jellyfish.egg-info/top_level.txt
reading manifest file 'dna_jellyfish.egg-info/SOURCES.txt'
writing manifest file 'dna_jellyfish.egg-info/SOURCES.txt'
Copying dna_jellyfish.egg-info to /<<PKGBUILDDIR>>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages/dna_jellyfish-0.0.1.egg-info
Skipping SOURCES.txt
running install_scripts
dh_auto_install --sourcedirectory=swig/perl5
cd swig/perl5 && make -j8 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr
make[2]: Entering directory '/<<PKGBUILDDIR>>/swig/perl5'
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so
make[2]: Leaving directory '/<<PKGBUILDDIR>>/swig/perl5'
ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so
-r-xr-xr-x 1 debusine-worker sbuild 1228136 Oct 24 05:20 debian/tmp/usr/lib/aarch64-linux-gnu/perl5/5.40/auto/jellyfish/jellyfish.so
if [ ! -e debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so ] ; then sleep 1; fi
chmod +w debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so
chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so
dh_install
d-shlibmove --commit \
--multiarch \
--devunversioned \
--movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp" usr/include/jellyfish \
--movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.h" usr/include/jellyfish \
--movedev config.h usr/include/jellyfish \
debian/tmp/usr/lib/*/libjellyfish-*.so
Library package automatic movement utility
set -e
install -d -m 755 debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu
install -d -m 755 debian/libjellyfish-2.0-2/usr/lib/aarch64-linux-gnu
mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu
mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu || true
mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2 debian/libjellyfish-2.0-2/usr/lib/aarch64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 debian/libjellyfish-2.0-2/usr/lib/aarch64-linux-gnu
PKGDEV=libjellyfish-2.0-dev
PKGSHL=libjellyfish-2.0-2
install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish
mv debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp debian/libjellyfish-2.0-dev/usr/include/jellyfish
install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish
mv debian/tmp/usr/include/jellyfish*/jellyfish/*.h debian/libjellyfish-2.0-dev/usr/include/jellyfish
install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish
mv config.h debian/libjellyfish-2.0-dev/usr/include/jellyfish
sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu/*.la
chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
debian/rules execute_after_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# Fix PACKAGE_NAME defined in config.h colliding with potential reverse
# dependencies autotools invocations, per lintian warning.
rm -vf debian/libjellyfish-2.0-dev/usr/include/jellyfish/config.h
removed 'debian/libjellyfish-2.0-dev/usr/include/jellyfish/config.h'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_python3 -a
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
debian/rules override_dh_missing
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# Python files are just installed
rm -rf debian/tmp/usr/lib/python3/dist-packages
# Necessary Perl files are just installed
rm -rf debian/tmp/usr/lib/perl/5.*
dh_missing
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.1-3+bd1_arm64.deb'.
dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.1-3+bd1_arm64.deb'.
dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.1-3+bd1_arm64.deb'.
dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.1-3+bd1_arm64.deb'.
dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.1-3+bd1_arm64.deb'.
dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.1-3+bd1_arm64.deb'.
dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.1-3+bd1_arm64.deb'.
dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.1-3+bd1_arm64.deb'.
dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.1-3+bd1_arm64.deb'.
dpkg-genbuildinfo --build=any -O../jellyfish_2.3.1-3+bd1_arm64.buildinfo
dpkg-genchanges --build=any -mDebusine Rebuild <debusine@example.net> -O../jellyfish_2.3.1-3+bd1_arm64.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2024-10-24T05:21:26Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
jellyfish_2.3.1-3+bd1_arm64.changes:
------------------------------------
Format: 1.8
Date: Thu, 24 Oct 2024 05:16:33 +0000
Source: jellyfish (2.3.1-3)
Binary: jellyfish jellyfish-dbgsym libjellyfish-2.0-2 libjellyfish-2.0-2-dbgsym libjellyfish-2.0-dev libjellyfish-perl libjellyfish-perl-dbgsym python3-dna-jellyfish python3-dna-jellyfish-dbgsym
Binary-Only: yes
Architecture: arm64
Version: 2.3.1-3+bd1
Distribution: sid
Urgency: low
Maintainer: Debusine Rebuild <debusine@example.net>
Changed-By: Debusine Rebuild <debusine@example.net>
Description:
jellyfish - count k-mers in DNA sequences
libjellyfish-2.0-2 - count k-mers in DNA sequences (dynamic library of jellyfish)
libjellyfish-2.0-dev - count k-mers in DNA sequences (development files of jellyfish)
libjellyfish-perl - count k-mers in DNA sequences (Perl bindings of jellyfish)
python3-dna-jellyfish - count k-mers in DNA sequences (Python bindings of jellyfish)
Changes:
jellyfish (2.3.1-3+bd1) sid; urgency=low, binary-only=yes
.
* Append +bd1 to version number; no source changes
* Binary-only non-maintainer upload for arm64; no source changes.
* Rebuild for python3.13
Checksums-Sha1:
808a1b09a794bf5e7055cf2c24707199c23083e1 7251400 jellyfish-dbgsym_2.3.1-3+bd1_arm64.deb
88fa5f755a027b4da98e1341a33965e4e366b2d5 11613 jellyfish_2.3.1-3+bd1_arm64.buildinfo
207673558e46f85d257f434ad1cc4c5142d1d508 726764 jellyfish_2.3.1-3+bd1_arm64.deb
ef37351e4c0fac1fd2ae46813a7bbe59815aabe8 529880 libjellyfish-2.0-2-dbgsym_2.3.1-3+bd1_arm64.deb
5d08d4e03dec519408133a7fee11816a121a98b7 61780 libjellyfish-2.0-2_2.3.1-3+bd1_arm64.deb
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cc489def978c94d1ff4653e6c793eb7859e4bce4 643068 python3-dna-jellyfish-dbgsym_2.3.1-3+bd1_arm64.deb
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d0f3401c821f9ee978ecfdce72415780 63904 python optional python3-dna-jellyfish_2.3.1-3+bd1_arm64.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: jellyfish (2.3.1-3)
Binary: jellyfish jellyfish-dbgsym libjellyfish-2.0-2 libjellyfish-2.0-2-dbgsym libjellyfish-2.0-dev libjellyfish-perl libjellyfish-perl-dbgsym python3-dna-jellyfish python3-dna-jellyfish-dbgsym
Architecture: arm64
Version: 2.3.1-3+bd1
Binary-Only-Changes:
jellyfish (2.3.1-3+bd1) sid; urgency=low, binary-only=yes
.
* Append +bd1 to version number; no source changes
* Binary-only non-maintainer upload for arm64; no source changes.
* Rebuild for python3.13
.
-- Debusine Rebuild <debusine@example.net> Thu, 24 Oct 2024 05:16:33 +0000
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Build-Origin: Debian
Build-Architecture: arm64
Build-Date: Thu, 24 Oct 2024 05:21:26 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
apt (= 2.9.10),
architecture-properties (= 0.2.3),
autoconf (= 2.72-3),
autoconf-archive (= 20220903-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.22.5-2),
autotools-dev (= 20220109.1),
base-files (= 13.5),
base-passwd (= 3.6.5),
bash (= 5.2.32-1+b2),
bc (= 1.07.1-4),
binutils (= 2.43.1-5),
binutils-aarch64-linux-gnu (= 2.43.1-5),
binutils-common (= 2.43.1-5),
bsdextrautils (= 2.40.2-9),
bsdutils (= 1:2.40.2-9),
build-essential (= 12.12),
bzip2 (= 1.0.8-6),
ca-certificates (= 20240203),
chrpath (= 0.16-2+b1),
coreutils (= 9.5-1),
cpp (= 4:14.2.0-1),
cpp-14 (= 14.2.0-7),
cpp-14-aarch64-linux-gnu (= 14.2.0-7),
cpp-aarch64-linux-gnu (= 4:14.2.0-1),
d-shlibs (= 0.107),
dash (= 0.5.12-9),
debconf (= 1.5.87),
debhelper (= 13.20),
debian-archive-keyring (= 2023.4),
debianutils (= 5.20),
dh-autoreconf (= 20),
dh-python (= 6.20240824),
dh-strip-nondeterminism (= 1.14.0-1),
diffutils (= 1:3.10-1),
dos2unix (= 7.5.2-1),
dpkg (= 1.22.11),
dpkg-dev (= 1.22.11),
dwz (= 0.15-1+b1),
file (= 1:5.45-3),
findutils (= 4.10.0-3),
g++ (= 4:14.2.0-1),
g++-14 (= 14.2.0-7),
g++-14-aarch64-linux-gnu (= 14.2.0-7),
g++-aarch64-linux-gnu (= 4:14.2.0-1),
gcc (= 4:14.2.0-1),
gcc-14 (= 14.2.0-7),
gcc-14-aarch64-linux-gnu (= 14.2.0-7),
gcc-14-base (= 14.2.0-7),
gcc-aarch64-linux-gnu (= 4:14.2.0-1),
gettext (= 0.22.5-2),
gettext-base (= 0.22.5-2),
gpgv (= 2.2.44-1),
grep (= 3.11-4),
groff-base (= 1.23.0-5),
gzip (= 1.12-1.1),
hostname (= 3.25),
init-system-helpers (= 1.67),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.2-2),
libapt-pkg6.0t64 (= 2.9.10),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 14.2.0-7),
libatomic1 (= 14.2.0-7),
libattr1 (= 1:2.5.2-2),
libaudit-common (= 1:4.0.1-1),
libaudit1 (= 1:4.0.1-1),
libbinutils (= 2.43.1-5),
libblkid1 (= 2.40.2-9),
libbrotli-dev (= 1.1.0-2+b4),
libbrotli1 (= 1.1.0-2+b4),
libbsd0 (= 0.12.2-2),
libbz2-1.0 (= 1.0.8-6),
libc-bin (= 2.40-3),
libc-dev-bin (= 2.40-3),
libc6 (= 2.40-3),
libc6-dev (= 2.40-3),
libcap-ng0 (= 0.8.5-3),
libcap2 (= 1:2.66-5),
libcc1-0 (= 14.2.0-7),
libcom-err2 (= 1.47.1-1),
libcrypt-dev (= 1:4.4.36-5),
libcrypt1 (= 1:4.4.36-5),
libctf-nobfd0 (= 2.43.1-5),
libctf0 (= 2.43.1-5),
libcurl3t64-gnutls (= 8.10.1-2),
libcurl4-gnutls-dev (= 8.10.1-2),
libdb5.3t64 (= 5.3.28+dfsg2-9),
libdebconfclient0 (= 0.272),
libdebhelper-perl (= 13.20),
libdeflate-dev (= 1.22-1),
libdeflate0 (= 1.22-1),
libdpkg-perl (= 1.22.11),
libedit2 (= 3.1-20240808-1),
libelf1t64 (= 0.192-4),
libevent-2.1-7t64 (= 2.1.12-stable-10),
libexpat1 (= 2.6.3-1),
libexpat1-dev (= 2.6.3-1),
libffi8 (= 3.4.6-1),
libfile-stripnondeterminism-perl (= 1.14.0-1),
libgcc-14-dev (= 14.2.0-7),
libgcc-s1 (= 14.2.0-7),
libgcrypt20 (= 1.11.0-6),
libgdbm-compat4t64 (= 1.24-2),
libgdbm6t64 (= 1.24-2),
libgmp-dev (= 2:6.3.0+dfsg-2+b1),
libgmp10 (= 2:6.3.0+dfsg-2+b1),
libgmpxx4ldbl (= 2:6.3.0+dfsg-2+b1),
libgnutls-dane0t64 (= 3.8.6-2),
libgnutls-openssl27t64 (= 3.8.6-2),
libgnutls28-dev (= 3.8.6-2),
libgnutls30t64 (= 3.8.6-2),
libgomp1 (= 14.2.0-7),
libgpg-error0 (= 1.50-4),
libgprofng0 (= 2.43.1-5),
libgssapi-krb5-2 (= 1.21.3-3),
libhogweed6t64 (= 3.10-1),
libhts-dev (= 1.20+ds-1),
libhts3t64 (= 1.20+ds-1),
libhtscodecs2 (= 1.6.1-1),
libhwasan0 (= 14.2.0-7),
libicu72 (= 72.1-5),
libidn2-0 (= 2.3.7-2),
libidn2-dev (= 2.3.7-2),
libisl23 (= 0.27-1),
libitm1 (= 14.2.0-7),
libjansson4 (= 2.14-2+b2),
libjs-jquery (= 3.6.1+dfsg+~3.5.14-1),
libjs-sphinxdoc (= 7.4.7-3),
libjs-underscore (= 1.13.4~dfsg+~1.11.4-3),
libk5crypto3 (= 1.21.3-3),
libkeyutils1 (= 1.6.3-3.1),
libkrb5-3 (= 1.21.3-3),
libkrb5support0 (= 1.21.3-3),
libldap-2.5-0 (= 2.5.18+dfsg-3+b1),
liblsan0 (= 14.2.0-7),
liblz4-1 (= 1.9.4-3),
liblzma-dev (= 5.6.2-2),
liblzma5 (= 5.6.2-2),
libmagic-mgc (= 1:5.45-3),
libmagic1t64 (= 1:5.45-3),
libmd0 (= 1.1.0-2),
libmount1 (= 2.40.2-9),
libmpc3 (= 1.3.1-1+b2),
libmpfr6 (= 4.2.1-1+b1),
libncurses6 (= 6.5-2),
libncursesw6 (= 6.5-2),
libnettle8t64 (= 3.10-1),
libnghttp2-14 (= 1.63.0-1),
libnghttp2-dev (= 1.63.0-1),
libnghttp3-9 (= 1.4.0-1),
libnghttp3-dev (= 1.4.0-1),
libngtcp2-16 (= 1.6.0-1),
libngtcp2-crypto-gnutls-dev (= 1.6.0-1),
libngtcp2-crypto-gnutls8 (= 1.6.0-1),
libngtcp2-dev (= 1.6.0-1),
libnsl2 (= 1.3.0-3+b2),
libp11-kit-dev (= 0.25.5-2),
libp11-kit0 (= 0.25.5-2),
libpam-modules (= 1.5.3-7),
libpam-modules-bin (= 1.5.3-7),
libpam-runtime (= 1.5.3-7),
libpam0g (= 1.5.3-7),
libpcre2-8-0 (= 10.42-4+b1),
libperl5.40 (= 5.40.0-6),
libpipeline1 (= 1.5.8-1),
libpkgconf3 (= 1.8.1-4),
libproc2-0 (= 2:4.0.4-6),
libpsl-dev (= 0.21.2-1.1),
libpsl5t64 (= 0.21.2-1.1),
libpython3-all-dev (= 3.12.6-1+debusine1),
libpython3-dev (= 3.12.6-1+debusine1),
libpython3-stdlib (= 3.12.6-1+debusine1),
libpython3.12-dev (= 3.12.7-1),
libpython3.12-minimal (= 3.12.7-1),
libpython3.12-stdlib (= 3.12.7-1),
libpython3.12t64 (= 3.12.7-1),
libpython3.13 (= 3.13.0-1),
libpython3.13-dev (= 3.13.0-1),
libpython3.13-minimal (= 3.13.0-1),
libpython3.13-stdlib (= 3.13.0-1),
libreadline8t64 (= 8.2-5),
librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b4),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4),
libruby (= 1:3.1+nmu1),
libruby3.1t64 (= 3.1.2-8.4),
libsasl2-2 (= 2.1.28+dfsg1-8),
libsasl2-modules-db (= 2.1.28+dfsg1-8),
libseccomp2 (= 2.5.5-1+b1),
libselinux1 (= 3.7-3),
libsframe1 (= 2.43.1-5),
libsmartcols1 (= 2.40.2-9),
libsqlite3-0 (= 3.46.1-1),
libssh2-1-dev (= 1.11.1-1),
libssh2-1t64 (= 1.11.1-1),
libssl-dev (= 3.3.2-1),
libssl3t64 (= 3.3.2-1),
libstdc++-14-dev (= 14.2.0-7),
libstdc++6 (= 14.2.0-7),
libsystemd0 (= 256.7-2),
libtasn1-6 (= 4.19.0-3+b2),
libtasn1-6-dev (= 4.19.0-3+b2),
libtinfo6 (= 6.5-2),
libtirpc-common (= 1.3.4+ds-1.3),
libtirpc3t64 (= 1.3.4+ds-1.3),
libtool (= 2.4.7-7),
libtsan2 (= 14.2.0-7),
libubsan1 (= 14.2.0-7),
libuchardet0 (= 0.0.8-1+b1),
libudev1 (= 256.7-2),
libunbound8 (= 1.22.0-1),
libunistring5 (= 1.2-1),
libuuid1 (= 2.40.2-9),
libxml2 (= 2.12.7+dfsg+really2.9.14-0.1),
libxxhash0 (= 0.8.2-2+b1),
libyaml-0-2 (= 0.2.5-1+b1),
libzstd-dev (= 1.5.6+dfsg-1),
libzstd1 (= 1.5.6+dfsg-1),
linux-libc-dev (= 6.11.4-1),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.13.0-1),
mawk (= 1.3.4.20240905-1),
media-types (= 10.1.0),
ncurses-base (= 6.5-2),
ncurses-bin (= 6.5-2),
netbase (= 6.4),
nettle-dev (= 3.10-1),
openssl (= 3.3.2-1),
openssl-provider-legacy (= 3.3.2-1),
patch (= 2.7.6-7),
perl (= 5.40.0-6),
perl-base (= 5.40.0-6),
perl-modules-5.40 (= 5.40.0-6),
pkgconf (= 1.8.1-4),
pkgconf-bin (= 1.8.1-4),
po-debconf (= 1.0.21+nmu1),
procps (= 2:4.0.4-6),
python3 (= 3.12.6-1+debusine1),
python3-all (= 3.12.6-1+debusine1),
python3-all-dev (= 3.12.6-1+debusine1),
python3-autocommand (= 2.2.2-3),
python3-dev (= 3.12.6-1+debusine1),
python3-inflect (= 7.3.1-2),
python3-jaraco.context (= 6.0.0-1),
python3-jaraco.functools (= 4.1.0-1),
python3-minimal (= 3.12.6-1+debusine1),
python3-more-itertools (= 10.5.0-1),
python3-pkg-resources (= 74.1.2-2),
python3-setuptools (= 74.1.2-2),
python3-typeguard (= 4.3.0-1),
python3-typing-extensions (= 4.12.2-2),
python3-zipp (= 3.20.2-1),
python3.12 (= 3.12.7-1),
python3.12-dev (= 3.12.7-1),
python3.12-minimal (= 3.12.7-1),
python3.13 (= 3.13.0-1),
python3.13-dev (= 3.13.0-1),
python3.13-minimal (= 3.13.0-1),
rake (= 13.2.1-1),
readline-common (= 8.2-5),
rpcsvc-proto (= 1.4.3-1),
ruby (= 1:3.1+nmu1),
ruby-net-telnet (= 0.2.0-1),
ruby-rubygems (= 3.4.20-1),
ruby-sdbm (= 1.0.0-5+b4),
ruby-webrick (= 1.8.1-1),
ruby-xmlrpc (= 0.3.3-2),
ruby3.1 (= 3.1.2-8.4),
rubygems-integration (= 1.18),
samtools (= 1.20-3),
sed (= 4.9-2),
sensible-utils (= 0.0.24),
swig (= 4.2.1-1),
sysvinit-utils (= 3.11-1),
tar (= 1.35+dfsg-3),
time (= 1.9-0.2),
tzdata (= 2024b-3),
util-linux (= 2.40.2-9),
xz-utils (= 5.6.2-2),
yaggo (= 1.5.11-1),
zlib1g (= 1:1.3.dfsg+really1.3.1-1),
zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1)
Environment:
DEB_BUILD_OPTIONS="parallel=8"
LANG="C.UTF-8"
LC_COLLATE="C.UTF-8"
LC_CTYPE="C.UTF-8"
SOURCE_DATE_EPOCH="1729746993"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
jellyfish-dbgsym_2.3.1-3+bd1_arm64.deb
--------------------------------------
new Debian package, version 2.0.
size 7251400 bytes: control archive=756 bytes.
520 bytes, 12 lines control
511 bytes, 5 lines md5sums
Package: jellyfish-dbgsym
Source: jellyfish (2.3.1-3)
Version: 2.3.1-3+bd1
Auto-Built-Package: debug-symbols
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7910
Depends: jellyfish (= 2.3.1-3+bd1)
Section: debug
Priority: optional
Description: debug symbols for jellyfish
Build-Ids: 7347c2b474ba8e38e3409eebdf6135273102df68 73a8544805e3ce53626f59d5ae884cb3c960cab4 9da559468bf0bae540c89198882a921448935ded d4df3b95924179cdf8fdd2382443495ef0b51865
drwxr-xr-x root/root 0 2024-10-24 05:16 ./
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/
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-rw-r--r-- root/root 1422504 2024-10-24 05:16 ./usr/lib/debug/.build-id/73/a8544805e3ce53626f59d5ae884cb3c960cab4.debug
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-rw-r--r-- root/root 77200 2024-10-24 05:16 ./usr/lib/debug/.build-id/d4/df3b95924179cdf8fdd2382443495ef0b51865.debug
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/debug/.dwz/aarch64-linux-gnu/
-rw-r--r-- root/root 79192 2024-10-24 05:16 ./usr/lib/debug/.dwz/aarch64-linux-gnu/jellyfish.debug
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-10-24 05:16 ./usr/share/doc/jellyfish-dbgsym -> jellyfish
jellyfish_2.3.1-3+bd1_arm64.deb
-------------------------------
new Debian package, version 2.0.
size 726764 bytes: control archive=1368 bytes.
1185 bytes, 24 lines control
988 bytes, 14 lines md5sums
Package: jellyfish
Source: jellyfish (2.3.1-3)
Version: 2.3.1-3+bd1
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2511
Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libhts3t64 (>= 1.17), libjellyfish-2.0-2 (= 2.3.1-3+bd1), libstdc++6 (>= 14)
Section: science
Priority: optional
Homepage: https://www.genome.umd.edu/jellyfish.html
Description: count k-mers in DNA sequences
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
drwxr-xr-x root/root 0 2024-10-24 05:16 ./
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/bin/
-rwxr-xr-x root/root 335104 2024-10-24 05:16 ./usr/bin/jellyfish
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/jellyfish/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/jellyfish/bin/
-rwxr-xr-x root/root 67976 2024-10-24 05:16 ./usr/lib/jellyfish/bin/fastq2sam
-rwxr-xr-x root/root 68176 2024-10-24 05:16 ./usr/lib/jellyfish/bin/generate_sequence
-rwxr-xr-x root/root 1837696 2024-10-24 05:16 ./usr/lib/jellyfish/bin/test_all
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/doc-base/
-rw-r--r-- root/root 987 2019-09-27 12:56 ./usr/share/doc-base/jellyfish.jellyfish
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/doc/jellyfish/
-rw-r--r-- root/root 321 2019-09-27 12:56 ./usr/share/doc/jellyfish/README.test
-rw-r--r-- root/root 222 2024-10-24 05:16 ./usr/share/doc/jellyfish/changelog.Debian.arm64.gz
-rw-r--r-- root/root 2778 2024-10-24 05:16 ./usr/share/doc/jellyfish/changelog.Debian.gz
-rw-r--r-- root/root 284 2023-12-06 21:50 ./usr/share/doc/jellyfish/changelog.gz
-rw-r--r-- root/root 6395 2024-03-19 17:20 ./usr/share/doc/jellyfish/copyright
-rw-r--r-- root/root 221453 2023-12-06 21:50 ./usr/share/doc/jellyfish/jellyfish.pdf.gz
-rw-r--r-- root/root 1665 2024-02-28 13:56 ./usr/share/doc/jellyfish/run-unit-test
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/lintian/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 144 2024-02-28 13:56 ./usr/share/lintian/overrides/jellyfish
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/man/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/man/man1/
-rw-r--r-- root/root 4554 2024-10-24 05:16 ./usr/share/man/man1/jellyfish.1.gz
libjellyfish-2.0-2-dbgsym_2.3.1-3+bd1_arm64.deb
-----------------------------------------------
new Debian package, version 2.0.
size 529880 bytes: control archive=568 bytes.
440 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libjellyfish-2.0-2-dbgsym
Source: jellyfish (2.3.1-3)
Version: 2.3.1-3+bd1
Auto-Built-Package: debug-symbols
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 560
Depends: libjellyfish-2.0-2 (= 2.3.1-3+bd1)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libjellyfish-2.0-2
Build-Ids: f8efab1abad4d4337f1c0fa1b404a00a0c82fc6c
drwxr-xr-x root/root 0 2024-10-24 05:16 ./
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/debug/.build-id/f8/
-rw-r--r-- root/root 562832 2024-10-24 05:16 ./usr/lib/debug/.build-id/f8/efab1abad4d4337f1c0fa1b404a00a0c82fc6c.debug
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-10-24 05:16 ./usr/share/doc/libjellyfish-2.0-2-dbgsym -> libjellyfish-2.0-2
libjellyfish-2.0-2_2.3.1-3+bd1_arm64.deb
----------------------------------------
new Debian package, version 2.0.
size 61780 bytes: control archive=1324 bytes.
1388 bytes, 31 lines control
504 bytes, 6 lines md5sums
49 bytes, 1 lines shlibs
66 bytes, 2 lines triggers
Package: libjellyfish-2.0-2
Source: jellyfish (2.3.1-3)
Version: 2.3.1-3+bd1
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 221
Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1)
Conflicts: libjellyfish-2.0-2t64
Replaces: libjellyfish-2.0-2t64
Provides: libjellfish-2.0-2t64 (= 2.3.1-3+bd1)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://www.genome.umd.edu/jellyfish.html
Description: count k-mers in DNA sequences (dynamic library of jellyfish)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
.
This package contains the dynamic library the main executable of
jellyfish is linked to.
drwxr-xr-x root/root 0 2024-10-24 05:16 ./
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/aarch64-linux-gnu/
lrwxrwxrwx root/root 0 2024-10-24 05:16 ./usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2 -> libjellyfish-2.0.so.2.0.0
-rw-r--r-- root/root 198688 2024-10-24 05:16 ./usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/doc/libjellyfish-2.0-2/
-rw-r--r-- root/root 222 2024-10-24 05:16 ./usr/share/doc/libjellyfish-2.0-2/changelog.Debian.arm64.gz
-rw-r--r-- root/root 2779 2024-10-24 05:16 ./usr/share/doc/libjellyfish-2.0-2/changelog.Debian.gz
-rw-r--r-- root/root 284 2023-12-06 21:50 ./usr/share/doc/libjellyfish-2.0-2/changelog.gz
-rw-r--r-- root/root 6395 2024-03-19 17:20 ./usr/share/doc/libjellyfish-2.0-2/copyright
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/lintian/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 178 2024-03-19 17:17 ./usr/share/lintian/overrides/libjellyfish-2.0-2
libjellyfish-2.0-dev_2.3.1-3+bd1_arm64.deb
------------------------------------------
new Debian package, version 2.0.
size 136100 bytes: control archive=2544 bytes.
1233 bytes, 27 lines control
4281 bytes, 57 lines md5sums
Package: libjellyfish-2.0-dev
Source: jellyfish (2.3.1-3)
Version: 2.3.1-3+bd1
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 688
Depends: libjellyfish-2.0-2 (= 2.3.1-3+bd1)
Section: libdevel
Priority: optional
Homepage: https://www.genome.umd.edu/jellyfish.html
Description: count k-mers in DNA sequences (development files of jellyfish)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
.
This package contains the development files (static library and
header files)
drwxr-xr-x root/root 0 2024-10-24 05:16 ./
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/include/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/include/jellyfish/
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-rw-r--r-- root/root 5898 2024-10-24 05:16 ./usr/include/jellyfish/atomic_bits_array.hpp
-rw-r--r-- root/root 4770 2024-10-24 05:16 ./usr/include/jellyfish/atomic_field.hpp
-rw-r--r-- root/root 1392 2024-10-24 05:16 ./usr/include/jellyfish/atomic_gcc.hpp
-rw-r--r-- root/root 272 2024-10-24 05:16 ./usr/include/jellyfish/backtrace.hpp
-rw-r--r-- root/root 6829 2024-10-24 05:16 ./usr/include/jellyfish/binary_dumper.hpp
-rw-r--r-- root/root 3480 2024-10-24 05:16 ./usr/include/jellyfish/bloom_common.hpp
-rw-r--r-- root/root 6778 2024-10-24 05:16 ./usr/include/jellyfish/bloom_counter2.hpp
-rw-r--r-- root/root 5447 2024-10-24 05:16 ./usr/include/jellyfish/bloom_filter.hpp
-rw-r--r-- root/root 5211 2024-10-24 05:16 ./usr/include/jellyfish/circular_buffer.hpp
-rw-r--r-- root/root 2408 2024-10-24 05:16 ./usr/include/jellyfish/compare_and_swap.hpp
-rw-r--r-- root/root 7472 2024-10-24 05:16 ./usr/include/jellyfish/cooperative_pool.hpp
-rw-r--r-- root/root 8494 2024-10-24 05:16 ./usr/include/jellyfish/cooperative_pool2.hpp
-rw-r--r-- root/root 4125 2024-10-24 05:16 ./usr/include/jellyfish/cpp_array.hpp
-rw-r--r-- root/root 2742 2024-10-24 05:16 ./usr/include/jellyfish/divisor.hpp
-rw-r--r-- root/root 2710 2024-10-24 05:16 ./usr/include/jellyfish/dumper.hpp
-rw-r--r-- root/root 2257 2024-10-24 05:16 ./usr/include/jellyfish/err.hpp
-rw-r--r-- root/root 4033 2024-10-24 05:16 ./usr/include/jellyfish/file_header.hpp
-rw-r--r-- root/root 4637 2024-10-24 05:16 ./usr/include/jellyfish/generator_manager.hpp
-rw-r--r-- root/root 6814 2024-10-24 05:16 ./usr/include/jellyfish/generic_file_header.hpp
-rw-r--r-- root/root 8326 2024-10-24 05:16 ./usr/include/jellyfish/hash_counter.hpp
-rw-r--r-- root/root 7025 2024-10-24 05:16 ./usr/include/jellyfish/int128.hpp
-rw-r--r-- root/root 1118 2024-10-24 05:16 ./usr/include/jellyfish/jellyfish.hpp
-rw-r--r-- root/root 61697 2024-10-24 05:16 ./usr/include/jellyfish/json.h
-rw-r--r-- root/root 40578 2024-10-24 05:16 ./usr/include/jellyfish/large_hash_array.hpp
-rw-r--r-- root/root 7564 2024-10-24 05:16 ./usr/include/jellyfish/large_hash_iterator.hpp
-rw-r--r-- root/root 4328 2024-10-24 05:16 ./usr/include/jellyfish/locks_pthread.hpp
-rw-r--r-- root/root 5181 2024-10-24 05:16 ./usr/include/jellyfish/mapped_file.hpp
-rw-r--r-- root/root 23839 2024-10-24 05:16 ./usr/include/jellyfish/mer_dna.hpp
-rw-r--r-- root/root 1296 2024-10-24 05:16 ./usr/include/jellyfish/mer_dna_bloom_counter.hpp
-rw-r--r-- root/root 3076 2024-10-24 05:16 ./usr/include/jellyfish/mer_heap.hpp
-rw-r--r-- root/root 2588 2024-10-24 05:16 ./usr/include/jellyfish/mer_iterator.hpp
-rw-r--r-- root/root 9371 2024-10-24 05:16 ./usr/include/jellyfish/mer_overlap_sequence_parser.hpp
-rw-r--r-- root/root 3247 2024-10-24 05:16 ./usr/include/jellyfish/mer_qual_iterator.hpp
-rw-r--r-- root/root 8066 2024-10-24 05:16 ./usr/include/jellyfish/misc.hpp
-rw-r--r-- root/root 10025 2024-10-24 05:16 ./usr/include/jellyfish/offsets_key_value.hpp
-rw-r--r-- root/root 960 2024-10-24 05:16 ./usr/include/jellyfish/parser_common.hpp
-rw-r--r-- root/root 12859 2024-10-24 05:16 ./usr/include/jellyfish/rectangular_binary_matrix.hpp
-rw-r--r-- root/root 2311 2024-10-24 05:16 ./usr/include/jellyfish/sam_format.hpp
-rw-r--r-- root/root 3504 2024-10-24 05:16 ./usr/include/jellyfish/simple_circular_buffer.hpp
-rw-r--r-- root/root 3346 2024-10-24 05:16 ./usr/include/jellyfish/sorted_dumper.hpp
-rw-r--r-- root/root 5069 2024-10-24 05:16 ./usr/include/jellyfish/stdio_filebuf.hpp
-rw-r--r-- root/root 602 2024-10-24 05:16 ./usr/include/jellyfish/storage.hpp
-rw-r--r-- root/root 2036 2024-10-24 05:16 ./usr/include/jellyfish/stream_iterator.hpp
-rw-r--r-- root/root 6318 2024-10-24 05:16 ./usr/include/jellyfish/stream_manager.hpp
-rw-r--r-- root/root 2063 2024-10-24 05:16 ./usr/include/jellyfish/text_dumper.hpp
-rw-r--r-- root/root 994 2024-10-24 05:16 ./usr/include/jellyfish/thread_exec.hpp
-rw-r--r-- root/root 1884 2024-10-24 05:16 ./usr/include/jellyfish/time.hpp
-rw-r--r-- root/root 1599 2024-10-24 05:16 ./usr/include/jellyfish/token_ring.hpp
-rw-r--r-- root/root 6761 2024-10-24 05:16 ./usr/include/jellyfish/whole_sequence_parser.hpp
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/aarch64-linux-gnu/
-rw-r--r-- root/root 314696 2024-10-24 05:16 ./usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a
-rw-r--r-- root/root 1006 2024-10-24 05:16 ./usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la
lrwxrwxrwx root/root 0 2024-10-24 05:16 ./usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so -> libjellyfish-2.0.so.2.0.0
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/aarch64-linux-gnu/pkgconfig/
-rw-r--r-- root/root 274 2024-10-24 05:16 ./usr/lib/aarch64-linux-gnu/pkgconfig/jellyfish-2.0.pc
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/doc/libjellyfish-2.0-dev/
-rw-r--r-- root/root 222 2024-10-24 05:16 ./usr/share/doc/libjellyfish-2.0-dev/changelog.Debian.arm64.gz
-rw-r--r-- root/root 2779 2024-10-24 05:16 ./usr/share/doc/libjellyfish-2.0-dev/changelog.Debian.gz
-rw-r--r-- root/root 284 2023-12-06 21:50 ./usr/share/doc/libjellyfish-2.0-dev/changelog.gz
-rw-r--r-- root/root 6395 2024-03-19 17:20 ./usr/share/doc/libjellyfish-2.0-dev/copyright
libjellyfish-perl-dbgsym_2.3.1-3+bd1_arm64.deb
----------------------------------------------
new Debian package, version 2.0.
size 357792 bytes: control archive=568 bytes.
437 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libjellyfish-perl-dbgsym
Source: jellyfish (2.3.1-3)
Version: 2.3.1-3+bd1
Auto-Built-Package: debug-symbols
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 379
Depends: libjellyfish-perl (= 2.3.1-3+bd1)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libjellyfish-perl
Build-Ids: 1996b932c6d41a373925f12358721f361e413ea9
drwxr-xr-x root/root 0 2024-10-24 05:16 ./
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/debug/.build-id/19/
-rw-r--r-- root/root 377456 2024-10-24 05:16 ./usr/lib/debug/.build-id/19/96b932c6d41a373925f12358721f361e413ea9.debug
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-10-24 05:16 ./usr/share/doc/libjellyfish-perl-dbgsym -> libjellyfish-perl
libjellyfish-perl_2.3.1-3+bd1_arm64.deb
---------------------------------------
new Debian package, version 2.0.
size 54124 bytes: control archive=1168 bytes.
1251 bytes, 27 lines control
495 bytes, 6 lines md5sums
Package: libjellyfish-perl
Source: jellyfish (2.3.1-3)
Version: 2.3.1-3+bd1
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 229
Depends: perl (>= 5.40.0-6), perlapi-5.40.0, libc6 (>= 2.38), libgcc-s1 (>= 3.0)
Section: perl
Priority: optional
Multi-Arch: same
Homepage: https://www.genome.umd.edu/jellyfish.html
Description: count k-mers in DNA sequences (Perl bindings of jellyfish)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
.
This package contains the Perl bindings of jellyfish.
drwxr-xr-x root/root 0 2024-10-24 05:16 ./
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/
drwxr-xr-x root/root 0 2024-10-24 05:16 ./usr/lib/aarch64-linux-gnu/
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python3-dna-jellyfish-dbgsym_2.3.1-3+bd1_arm64.deb
--------------------------------------------------
new Debian package, version 2.0.
size 643068 bytes: control archive=656 bytes.
473 bytes, 12 lines control
311 bytes, 3 lines md5sums
Package: python3-dna-jellyfish-dbgsym
Source: jellyfish (2.3.1-3)
Version: 2.3.1-3+bd1
Auto-Built-Package: debug-symbols
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 700
Depends: python3-dna-jellyfish (= 2.3.1-3+bd1)
Section: debug
Priority: optional
Description: debug symbols for python3-dna-jellyfish
Build-Ids: 930cf4142112f0e5d944d3f38d21143287985ea2 df235ce823cebd4fe7abe42c39c92982518d2ae5
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lrwxrwxrwx root/root 0 2024-10-24 05:16 ./usr/share/doc/python3-dna-jellyfish-dbgsym -> python3-dna-jellyfish
python3-dna-jellyfish_2.3.1-3+bd1_arm64.deb
-------------------------------------------
new Debian package, version 2.0.
size 63904 bytes: control archive=1620 bytes.
1313 bytes, 26 lines control
977 bytes, 10 lines md5sums
289 bytes, 12 lines * postinst #!/bin/sh
402 bytes, 12 lines * prerm #!/bin/sh
Package: python3-dna-jellyfish
Source: jellyfish (2.3.1-3)
Version: 2.3.1-3+bd1
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 438
Depends: python3 (<< 3.14), python3 (>= 3.12~), python3:any, libc6 (>= 2.38), libgcc-s1 (>= 3.0), libjellyfish-2.0-2 (>= 2.3.1), libstdc++6 (>= 13.1)
Section: python
Priority: optional
Homepage: https://www.genome.umd.edu/jellyfish.html
Description: count k-mers in DNA sequences (Python bindings of jellyfish)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
.
This package contains the Python bindings of jellyfish.
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-rw-r--r-- root/root 6395 2024-03-19 17:20 ./usr/share/doc/python3-dna-jellyfish/copyright
lintian
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Build Architecture: arm64
Build Type: any
Build-Space: 1793580
Build-Time: 293
Distribution: sid
Host Architecture: arm64
Install-Time: 40
Job: /tmp/debusine-fetch-exec-upload-8aiaj_tc/jellyfish_2.3.1-3.dsc
Lintian: pass
Machine Architecture: arm64
Package: jellyfish
Package-Time: 370
Source-Version: 2.3.1-3
Space: 1793580
Status: successful
Version: 2.3.1-3+bd1
--------------------------------------------------------------------------------
Finished at 2024-10-24T05:21:26Z
Build needed 00:06:10, 1793580k disk space