rapmap →
0.15.0+dfsg-2 →
armhf → 2022-06-19 14:37:31
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| rapmap 0.15.0+dfsg-2 (armhf) Sun, 19 Jun 2022 14:26:35 +0000 |
+==============================================================================+
Package: rapmap
Version: 0.15.0+dfsg-2
Source Version: 0.15.0+dfsg-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-0a4aa5d0-06a9-45c8-94d1-d89eadf74722' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/rapmap-BFMkfz/resolver-Dncv0H' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.1 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.0 MB]
Fetched 27.0 MB in 15s (1788 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'rapmap' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/rapmap.git
Please use:
git clone https://salsa.debian.org/med-team/rapmap.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 642 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main rapmap 0.15.0+dfsg-2 (dsc) [2347 B]
Get:2 http://172.17.4.1/private bookworm-staging/main rapmap 0.15.0+dfsg-2 (tar) [625 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main rapmap 0.15.0+dfsg-2 (diff) [14.8 kB]
Fetched 642 kB in 0s (3642 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/rapmap-BFMkfz/rapmap-0.15.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/rapmap-BFMkfz' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libdivsufsort-dev, libcereal-dev, libjellyfish-2.0-dev, libjemalloc-dev, libsimde-dev, libsparsehash-dev, libspdlog-dev, libtclap-dev, pkg-config, python3-markdown, python3, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libdivsufsort-dev, libcereal-dev, libjellyfish-2.0-dev, libjemalloc-dev, libsimde-dev, libsparsehash-dev, libspdlog-dev, libtclap-dev, pkg-config, python3-markdown, python3, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [460 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [544 B]
Fetched 1961 B in 0s (36.2 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils catch2 cmake
cmake-data debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism
dwz emacsen-common file gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libarchive13 libbrotli1 libcereal-dev libcurl4
libdebhelper-perl libdivsufsort-dev libdivsufsort3 libelf1 libexpat1
libfile-stripnondeterminism-perl libfmt-dev libfmt8 libglib2.0-0 libicu71
libjellyfish-2.0-2 libjellyfish-2.0-dev libjemalloc-dev libjemalloc2
libjsoncpp25 libmagic-mgc libmagic1 libmpdec3 libncurses6 libncursesw6
libnghttp2-14 libpipeline1 libprocps8 libpsl5 libpython3-stdlib
libpython3.10-minimal libpython3.10-stdlib librhash0 librtmp1 libsigsegv2
libsimde-dev libsparsehash-dev libspdlog-dev libspdlog1 libssh2-1 libssl3
libsub-override-perl libtclap-dev libtinfo6 libtool libuchardet0 libuv1
libxml2 m4 man-db media-types pkg-config po-debconf procps python3
python3-importlib-metadata python3-markdown python3-minimal
python3-more-itertools python3-zipp python3.10 python3.10-minimal
rapidjson-dev zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build
cmake-format dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
lrzip libfmt-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl python3-doc python3-tk
python3-venv python-markdown-doc python3.10-venv python3.10-doc
binfmt-support rapidjson-doc
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl psmisc python3-pygments python3-yaml
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils catch2 cmake
cmake-data debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism
dwz emacsen-common file gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libarchive13 libbrotli1 libcereal-dev libcurl4
libdebhelper-perl libdivsufsort-dev libdivsufsort3 libelf1 libexpat1
libfile-stripnondeterminism-perl libfmt-dev libfmt8 libglib2.0-0 libicu71
libjellyfish-2.0-2 libjellyfish-2.0-dev libjemalloc-dev libjemalloc2
libjsoncpp25 libmagic-mgc libmagic1 libmpdec3 libncurses6 libnghttp2-14
libpipeline1 libprocps8 libpsl5 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib librhash0 librtmp1 libsigsegv2 libsimde-dev
libsparsehash-dev libspdlog-dev libspdlog1 libssh2-1 libssl3
libsub-override-perl libtclap-dev libtool libuchardet0 libuv1 libxml2 m4
man-db media-types pkg-config po-debconf procps python3
python3-importlib-metadata python3-markdown python3-minimal
python3-more-itertools python3-zipp python3.10 python3.10-minimal
rapidjson-dev sbuild-build-depends-main-dummy zlib1g-dev
The following packages will be upgraded:
libncursesw6 libtinfo6 zlib1g
3 upgraded, 82 newly installed, 0 to remove and 70 not upgraded.
Need to get 40.4 MB of archives.
After this operation, 163 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [964 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libssl3 armhf 3.0.3-7 [1645 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.5-1+b1 [815 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.8-1 [84.1 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-4+b2 [84.5 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.5-1+b1 [1637 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.4-1+b1 [38.9 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libtinfo6 armhf 6.3+20220423-2 [337 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libncursesw6 armhf 6.3+20220423-2 [104 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.5-1+b1 [1626 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.5-1+b1 [542 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.4-1+b1 [21.9 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.4-1+b1 [38.4 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38-4 [137 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-1 [33.7 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-1 [1362 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-7 [60.7 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-7 [475 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-6 [171 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-6 [510 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf catch2 armhf 2.13.9-1 [436 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libarchive13 armhf 3.6.0-1 [306 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.47.0-1+b1 [65.3 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.83.1-2 [317 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp25 armhf 1.9.5-4 [66.7 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf librhash0 armhf 1.4.2-1 [141 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libuv1 armhf 1.44.1-2+rpi1 [124 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf dh-elpa-helper all 2.0.10 [11.3 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf emacsen-common all 3.0.4 [19.3 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf cmake-data all 3.23.2-1 [1939 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf cmake armhf 3.23.2-1 [3551 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.7.1 [195 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-3 [10.4 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-1 [175 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-6 [1214 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.7.1 [1071 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf rapidjson-dev all 1.1.0+dfsg2-7 [98.9 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libcereal-dev all 1.3.1+dfsg-1 [221 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libdivsufsort3 armhf 2.0.1-5 [43.2 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libdivsufsort-dev armhf 2.0.1-5 [19.1 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libfmt8 armhf 8.1.1+ds1-2 [99.3 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libfmt-dev armhf 8.1.1+ds1-2 [164 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.72.2-2 [1231 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libjellyfish-2.0-2 armhf 2.3.0-13 [56.6 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libjellyfish-2.0-dev armhf 2.3.0-13 [128 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libjemalloc2 armhf 5.2.1-4 [188 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libjemalloc-dev armhf 5.2.1-4 [416 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libsimde-dev all 0.7.2-6 [259 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libspdlog1 armhf 1:1.9.2+ds-0.2 [99.2 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libspdlog-dev armhf 1:1.9.2+ds-0.2 [183 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libtclap-dev armhf 1.2.5-1 [3359 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf python3-more-itertools all 8.10.0-2 [53.0 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf python3-zipp all 1.0.0-4 [6160 B]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf python3-importlib-metadata all 4.6.4-1 [22.5 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf python3-markdown all 3.3.7-1 [71.7 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4+b2 [183 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking zlib1g:armhf (1:1.2.11.dfsg-4+b2) over (1:1.2.11.dfsg-4) ...
Setting up zlib1g:armhf (1:1.2.11.dfsg-4+b2) ...
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Setting up libpython3.10-minimal:armhf (3.10.5-1+b1) ...
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Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libspdlog1:armhf (1:1.9.2+ds-0.2) ...
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Setting up libssh2-1:armhf (1.10.0-3+b1) ...
Setting up cmake-data (3.23.2-1) ...
Setting up libdivsufsort3:armhf (2.0.1-5) ...
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Setting up libpython3.10-stdlib:armhf (3.10.5-1+b1) ...
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Setting up libpython3-stdlib:armhf (3.10.4-1+b1) ...
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 python3.10 (3.10.5-1+b1) ...
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Setting up man-db (2.10.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up cmake (3.23.2-1) ...
Setting up python3-more-itertools (8.10.0-2) ...
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Setting up python3-zipp (1.0.0-4) ...
Setting up python3-importlib-metadata (4.6.4-1) ...
Setting up python3-markdown (3.3.7-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.33-7+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.38-3+rpi1 dpkg-dev_1.21.7+rpi1 g++-11_11.2.0-20+rpi1 gcc-11_11.2.0-20+rpi1 libc6-dev_2.33-7+rpi1 libstdc++-11-dev_11.2.0-20+rpi1 libstdc++6_12-20220319-1+rpi1 linux-libc-dev_5.16.18-1+rpi1
Package versions: adduser_3.121 apt_2.4.5 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.5.52 bash_5.1-6 binutils_2.38-3+rpi1 binutils-arm-linux-gnueabihf_2.38-3+rpi1 binutils-common_2.38-3+rpi1 bsdextrautils_2.38-4 bsdutils_1:2.38-4 build-essential_12.9 bzip2_1.0.8-5 catch2_2.13.9-1 cmake_3.23.2-1 cmake-data_3.23.2-1 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-20+rpi1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.7.1 debianutils_5.7-0.1 dh-autoreconf_20 dh-elpa-helper_2.0.10 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-3+b1 dpkg_1.21.7+rpi1 dpkg-dev_1.21.7+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 emacsen-common_3.0.4 fakeroot_1.28-1 file_1:5.41-4 findutils_4.9.0-2 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-20+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-20+rpi1 gcc-11-base_11.2.0-20+rpi1 gcc-12-base_12-20220319-1+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-6 gettext-base_0.21-6 gnupg_2.2.27-3 gnupg-l10n_2.2.27-3 gnupg-utils_2.2.27-3+b1 gpg_2.2.27-3+b1 gpg-agent_2.2.27-3+b1 gpg-wks-client_2.2.27-3+b1 gpg-wks-server_2.2.27-3+b1 gpgconf_2.2.27-3+b1 gpgsm_2.2.27-3+b1 gpgv_2.2.27-3+b1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 init-system-helpers_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.4.5 libarchive-zip-perl_1.68-1 libarchive13_3.6.0-1 libasan6_11.2.0-20+rpi1 libassuan0_2.5.5-1 libatomic1_12-20220319-1+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbinutils_2.38-3+rpi1 libblkid1_2.38-4 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5 libc-bin_2.33-7+rpi1 libc-dev-bin_2.33-7+rpi1 libc6_2.33-7+rpi1 libc6-dev_2.33-7+rpi1 libcap-ng0_0.7.9-2.2+b2 libcap2_1:2.44-1 libcc1-0_12-20220319-1+rpi1 libcereal-dev_1.3.1+dfsg-1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.38-3+rpi1 libctf0_2.38-3+rpi1 libcurl4_7.83.1-2 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.262 libdebhelper-perl_13.7.1 libdivsufsort-dev_2.0.1-5 libdivsufsort3_2.0.1-5 libdpkg-perl_1.21.7+rpi1 libelf1_0.187-1 libexpat1_2.4.8-1 libext2fs2_1.46.5-2 libfakeroot_1.28-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libfmt-dev_8.1.1+ds1-2 libfmt8_8.1.1+ds1-2 libgcc-11-dev_11.2.0-20+rpi1 libgcc-s1_12-20220319-1+rpi1 libgcrypt20_1.10.1-2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libglib2.0-0_2.72.2-2 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.4-2 libgomp1_12-20220319-1+rpi1 libgpg-error0_1.43-3 libgssapi-krb5-2_1.19.2-2+b2 libhogweed6_3.7.3-1 libicu71_71.1-3 libidn2-0_2.3.2-2 libisl23_0.24-2 libjellyfish-2.0-2_2.3.0-13 libjellyfish-2.0-dev_2.3.0-13 libjemalloc-dev_5.2.1-4 libjemalloc2_5.2.1-4 libjsoncpp25_1.9.5-4 libk5crypto3_1.19.2-2+b2 libkeyutils1_1.6.1-3+rpi1 libkrb5-3_1.19.2-2+b2 libkrb5support0_1.19.2-2+b2 libksba8_1.6.0-2 libldap-2.5-0_2.5.11+dfsg-1+rpi1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38-4 libmpc3_1.2.1-2 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.7.3-1 libnghttp2-14_1.47.0-1+b1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-4 libpcre3_2:8.39-14 libperl5.32_5.32.1-6 libperl5.34_5.34.0-4 libpipeline1_1.5.6-1 libprocps8_2:3.3.17-7 libpsl5_0.21.0-1.2 libpython3-stdlib_3.10.4-1+b1 libpython3.10-minimal_3.10.5-1+b1 libpython3.10-stdlib_3.10.5-1+b1 libreadline8_8.1.2-1.2 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-4 libsasl2-modules-db_2.1.28+dfsg-4 libseccomp2_2.5.3-2+rpi1+b1 libselinux1_3.3-1+b1 libsemanage-common_3.3-1 libsemanage2_3.3-1+b1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.14-1 libsimde-dev_0.7.2-6 libsmartcols1_2.38-4 libsparsehash-dev_2.0.3-2 libspdlog-dev_1:1.9.2+ds-0.2 libspdlog1_1:1.9.2+ds-0.2 libsqlite3-0_3.38.2-1 libss2_1.46.5-2 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1n-1 libssl3_3.0.3-7 libstdc++-11-dev_11.2.0-20+rpi1 libstdc++6_12-20220319-1+rpi1 libsub-override-perl_0.09-3 libsystemd0_250.4-1+rpi1 libtasn1-6_4.18.0-4 libtclap-dev_1.2.5-1 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.7-4 libubsan1_12-20220319-1+rpi1 libuchardet0_0.0.7-1 libudev1_250.4-1+rpi1 libunistring2_1.0-1 libuuid1_2.38-4 libuv1_1.44.1-2+rpi1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.16.18-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3 media-types_8.0.0 mount_2.38-4 ncurses-base_6.3-2 ncurses-bin_6.3-2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-4 perl-base_5.34.0-4 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-4 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 procps_2:3.3.17-7 python3_3.10.4-1+b1 python3-importlib-metadata_4.6.4-1 python3-markdown_3.3.7-1 python3-minimal_3.10.4-1+b1 python3-more-itertools_8.10.0-2 python3-zipp_1.0.0-4 python3.10_3.10.5-1+b1 python3.10-minimal_3.10.5-1+b1 rapidjson-dev_1.1.0+dfsg2-7 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.03-1 tar_1.34+dfsg-1 tzdata_2022a-1 util-linux_2.37.3-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4+b2 zlib1g-dev_1:1.2.11.dfsg-4+b2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: rapmap
Binary: rapmap, rapmap-example-data, rapmap-dev
Architecture: any all
Version: 0.15.0+dfsg-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Michael R. Crusoe <crusoe@debian.org>
Homepage: https://github.com/COMBINE-lab/RapMap
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/rapmap
Vcs-Git: https://salsa.debian.org/med-team/rapmap.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libdivsufsort-dev, libcereal-dev, libjellyfish-2.0-dev, libjemalloc-dev, libsimde-dev, libsparsehash-dev, libspdlog-dev, libtclap-dev, pkg-config, python3-markdown, python3
Package-List:
rapmap deb science optional arch=any
rapmap-dev deb science optional arch=all
rapmap-example-data deb science optional arch=all
Checksums-Sha1:
0c4a16003c0d2fe77679260ebdb6e21792f862f0 624916 rapmap_0.15.0+dfsg.orig.tar.xz
4488a8d41d12d2eecc8fd3e68834fa396e219120 14772 rapmap_0.15.0+dfsg-2.debian.tar.xz
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ce54955a604d6630dff2f33d31f5d69915b5403bac61b6611d6db26909d5128e 14772 rapmap_0.15.0+dfsg-2.debian.tar.xz
Files:
c52551692c7480f0c1a46478595dd24b 624916 rapmap_0.15.0+dfsg.orig.tar.xz
176940f31735987b02937689ba641fdd 14772 rapmap_0.15.0+dfsg-2.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.jKCZTIVj/trustedkeys.kbx': General error
gpgv: Signature made Tue Oct 12 10:10:36 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./rapmap_0.15.0+dfsg-2.dsc
dpkg-source: info: extracting rapmap in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking rapmap_0.15.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking rapmap_0.15.0+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use-debian-libs.patch
dpkg-source: info: applying use_shared_libs.patch
dpkg-source: info: applying avoid_privacy_breach.patch
dpkg-source: info: applying spelling
dpkg-source: info: applying portable_pause
dpkg-source: info: applying no_gomp_needed
dpkg-source: info: applying simde
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=7b33f05927d544f8acb7289c691791af
JOURNAL_STREAM=8:24067
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-0a4aa5d0-06a9-45c8-94d1-d89eadf74722
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c77648
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package rapmap
dpkg-buildpackage: info: source version 0.15.0+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean README.html sample_data/sample_quasi_index/ sample_data/sample_quasi_index_ph/ sample_data/sample_quasi_map.sam sample_data/sample_quasi_map_ph.sam
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true
cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true ..
CC: gcc
CC version:
-- The C compiler identification is GNU 11.2.0
-- The CXX compiler identification is GNU 11.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
version: 0.6.0
-- DISABLING NATIVE ARCH.
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
Making Default build type
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Found Cereal: /usr/include (Required is at least version "1.2.2")
-- Cereal found (include: /usr/include)
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2")
-- Found Jemalloc: /usr/lib/arm-linux-gnueabihf/libjemalloc.so (found version "5.2.1-0-gea6b3e973b477b8061e0076bb257dbd7f3faa756")
Found Jemalloc library --- using this memory allocator
CPACK_SOURCE_IGNORE_FILES = .git/
CMAKE_SYSTEM_PROCESSOR: armv7l
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
JELLYFISH_ROOT
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/depend
make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/build
make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 7%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o
[ 7%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o
[ 11%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o
[ 15%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/digestpp -I/<<PKGBUILDDIR>>/external -I/<<PKGBUILDDIR>>/external/cereal/include -I/<<PKGBUILDDIR>>/external/install/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /<<PKGBUILDDIR>>/src/ksw2pp/ksw2_extf2_sse.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /<<PKGBUILDDIR>>/src/ksw2pp/kalloc.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/digestpp -I/<<PKGBUILDDIR>>/external -I/<<PKGBUILDDIR>>/external/cereal/include -I/<<PKGBUILDDIR>>/external/install/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /<<PKGBUILDDIR>>/src/ksw2pp/ksw2_extd2_sse.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/digestpp -I/<<PKGBUILDDIR>>/external -I/<<PKGBUILDDIR>>/external/cereal/include -I/<<PKGBUILDDIR>>/external/install/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /<<PKGBUILDDIR>>/src/ksw2pp/ksw2_extz2_sse.c
/<<PKGBUILDDIR>>/src/ksw2pp/kalloc.c: In function ‘morecore’:
/<<PKGBUILDDIR>>/src/ksw2pp/kalloc.c:49:47: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
49 | fprintf(stderr, "[morecore] %lu bytes requested but not available.\n", rnu * sizeof(size_t));
| ~~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
/<<PKGBUILDDIR>>/src/ksw2pp/kalloc.c: In function ‘km_stat’:
/<<PKGBUILDDIR>>/src/ksw2pp/kalloc.c:212:42: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
212 | fprintf(stderr, "[kr_stat] tot=%lu, free=%lu, n_block=%u, max_block=%lu, frag_len=%.3fK\n",
| ~~^
| |
| long unsigned int
| %u
213 | km->total_allocated, n_units * sizeof(size_t), n_blocks, max_block * sizeof(size_t), frag);
| ~~~~~~~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
/<<PKGBUILDDIR>>/src/ksw2pp/kalloc.c:212:52: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘unsigned int’ [-Wformat=]
212 | fprintf(stderr, "[kr_stat] tot=%lu, free=%lu, n_block=%u, max_block=%lu, frag_len=%.3fK\n",
| ~~^
| |
| long unsigned int
| %u
213 | km->total_allocated, n_units * sizeof(size_t), n_blocks, max_block * sizeof(size_t), frag);
| ~~~~~~~~~~~~~~~~~~~~~~~~
| |
| unsigned int
/<<PKGBUILDDIR>>/src/ksw2pp/kalloc.c:212:79: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
212 | fprintf(stderr, "[kr_stat] tot=%lu, free=%lu, n_block=%u, max_block=%lu, frag_len=%.3fK\n",
| ~~^
| |
| long unsigned int
| %u
213 | km->total_allocated, n_units * sizeof(size_t), n_blocks, max_block * sizeof(size_t), frag);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
[ 19%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /<<PKGBUILDDIR>>/src/ksw2pp/ksw2_extd.c
[ 23%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /<<PKGBUILDDIR>>/src/ksw2pp/ksw2_extz.c
[ 26%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /<<PKGBUILDDIR>>/src/ksw2pp/ksw2_gg.c
[ 30%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /<<PKGBUILDDIR>>/src/ksw2pp/ksw2_gg2.c
[ 34%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /<<PKGBUILDDIR>>/src/ksw2pp/ksw2_gg2_sse.c
[ 38%] Building CXX object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /<<PKGBUILDDIR>>/src/ksw2pp/KSW2Aligner.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 38%] Built target ksw2pp_basic
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 38%] Built target ksw2pp_sse2
make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 42%] Linking CXX static library libksw2pp.a
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1
/usr/bin/ar qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o
/usr/bin/ranlib libksw2pp.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 42%] Built target ksw2pp
make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/CMakeFiles/rapmap.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 46%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o
[ 50%] Building CXX object src/CMakeFiles/rapmap.dir/RapMap.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/digestpp -I/<<PKGBUILDDIR>>/external -I/<<PKGBUILDDIR>>/external/cereal/include -I/<<PKGBUILDDIR>>/external/install/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -c /<<PKGBUILDDIR>>/src/RapMapSAIndexer.cpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/digestpp -I/<<PKGBUILDDIR>>/external -I/<<PKGBUILDDIR>>/external/cereal/include -I/<<PKGBUILDDIR>>/external/install/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMap.cpp.o -MF CMakeFiles/rapmap.dir/RapMap.cpp.o.d -o CMakeFiles/rapmap.dir/RapMap.cpp.o -c /<<PKGBUILDDIR>>/src/RapMap.cpp
[ 53%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/digestpp -I/<<PKGBUILDDIR>>/external -I/<<PKGBUILDDIR>>/external/cereal/include -I/<<PKGBUILDDIR>>/external/install/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o -MF CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o -c /<<PKGBUILDDIR>>/src/RapMapSAMapper.cpp
[ 57%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapUtils.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/digestpp -I/<<PKGBUILDDIR>>/external -I/<<PKGBUILDDIR>>/external/cereal/include -I/<<PKGBUILDDIR>>/external/install/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -std=c++14 -MD -MT src/CMakeFiles/rapmap.dir/RapMapUtils.cpp.o -MF CMakeFiles/rapmap.dir/RapMapUtils.cpp.o.d -o CMakeFiles/rapmap.dir/RapMapUtils.cpp.o -c /<<PKGBUILDDIR>>/src/RapMapUtils.cpp
In file included from /<<PKGBUILDDIR>>/include/BooMap.hpp:4,
from /<<PKGBUILDDIR>>/src/RapMapUtils.cpp:32:
/<<PKGBUILDDIR>>/include/BooPHF.hpp: In function ‘uint64_t boomphf::fastrange64(uint64_t, uint64_t)’:
/<<PKGBUILDDIR>>/include/BooPHF.hpp:818:37: error: ‘__uint128_t’ was not declared in this scope; did you mean ‘__uint8_t’?
818 | return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
| ^~~~~~~~~~~
| __uint8_t
/<<PKGBUILDDIR>>/include/BooPHF.hpp:818:49: error: expected ‘)’ before ‘word’
818 | return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
| ~ ^~~~
| )
/<<PKGBUILDDIR>>/include/BooPHF.hpp:818:78: error: expected ‘)’ before ‘;’ token
818 | return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
| ~ ^
| )
In file included from /<<PKGBUILDDIR>>/include/BooMap.hpp:4,
from /<<PKGBUILDDIR>>/src/RapMapSAIndexer.cpp:51:
/<<PKGBUILDDIR>>/include/BooPHF.hpp: In function ‘uint64_t boomphf::fastrange64(uint64_t, uint64_t)’:
/<<PKGBUILDDIR>>/include/BooPHF.hpp:818:37: error: ‘__uint128_t’ was not declared in this scope; did you mean ‘__uint8_t’?
818 | return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
| ^~~~~~~~~~~
| __uint8_t
/<<PKGBUILDDIR>>/include/BooPHF.hpp:818:49: error: expected ‘)’ before ‘word’
818 | return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
| ~ ^~~~
| )
/<<PKGBUILDDIR>>/include/BooPHF.hpp:818:78: error: expected ‘)’ before ‘;’ token
818 | return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
| ~ ^
| )
In file included from /<<PKGBUILDDIR>>/include/zstr/zstr.hpp:16,
from /<<PKGBUILDDIR>>/src/RapMapSAMapper.cpp:62:
/<<PKGBUILDDIR>>/include/zstr/strict_fstream.hpp: In static member function ‘static void strict_fstream::detail::static_method_holder::check_peek(std::istream*, const string&, std::ios_base::openmode)’:
/<<PKGBUILDDIR>>/include/zstr/strict_fstream.hpp:128:39: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=]
128 | catch (std::ios_base::failure e) {}
| ^
In file included from /<<PKGBUILDDIR>>/include/BooMap.hpp:4,
from /<<PKGBUILDDIR>>/src/RapMapSAMapper.cpp:70:
/<<PKGBUILDDIR>>/include/BooPHF.hpp: In function ‘uint64_t boomphf::fastrange64(uint64_t, uint64_t)’:
/<<PKGBUILDDIR>>/include/BooPHF.hpp:818:37: error: ‘__uint128_t’ was not declared in this scope; did you mean ‘__uint8_t’?
818 | return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
| ^~~~~~~~~~~
| __uint8_t
/<<PKGBUILDDIR>>/include/BooPHF.hpp:818:49: error: expected ‘)’ before ‘word’
818 | return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
| ~ ^~~~
| )
/<<PKGBUILDDIR>>/include/BooPHF.hpp:818:78: error: expected ‘)’ before ‘;’ token
818 | return (uint64_t)(((__uint128_t)word * (__uint128_t)p) >> 64);
| ~ ^
| )
At global scope:
cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics
make[4]: *** [src/CMakeFiles/rapmap.dir/build.make:107: src/CMakeFiles/rapmap.dir/RapMapUtils.cpp.o] Error 1
make[4]: *** Waiting for unfinished jobs....
At global scope:
cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics
make[4]: *** [src/CMakeFiles/rapmap.dir/build.make:93: src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o] Error 1
At global scope:
cc1plus: note: unrecognized command-line option ‘-Wno-unused-local-typedef’ may have been intended to silence earlier diagnostics
make[4]: *** [src/CMakeFiles/rapmap.dir/build.make:121: src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: *** [CMakeFiles/Makefile2:134: src/CMakeFiles/rapmap.dir/all] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
dh_auto_build: error: cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:22: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:16: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2022-06-19T14:37:27Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 8856
Build-Time: 45
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 564
Job: rapmap_0.15.0+dfsg-2
Machine Architecture: armhf
Package: rapmap
Package-Time: 652
Source-Version: 0.15.0+dfsg-2
Space: 8856
Status: attempted
Version: 0.15.0+dfsg-2
--------------------------------------------------------------------------------
Finished at 2022-06-19T14:37:27Z
Build needed 00:10:52, 8856k disk space