racon →
1.4.21-1 →
armhf → 2021-09-04 08:10:26
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| racon 1.4.21-1 (armhf) Sat, 04 Sep 2021 07:26:40 +0000 |
+==============================================================================+
Package: racon
Version: 1.4.21-1
Source Version: 1.4.21-1
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-3169e2c3-9c18-4f42-84d9-597a788e0ef6' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/racon-kIosGj/resolver-r9195A' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.3 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.7 MB in 10s (2506 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'racon' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/racon.git
Please use:
git clone https://salsa.debian.org/med-team/racon.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 3092 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main racon 1.4.21-1 (dsc) [2096 B]
Get:2 http://172.17.0.1/private bookworm-staging/main racon 1.4.21-1 (tar) [3083 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main racon 1.4.21-1 (diff) [6332 B]
Fetched 3092 kB in 1s (3428 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/racon-kIosGj/racon-1.4.21' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/racon-kIosGj' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), cmake, libgtest-dev, libbioparser-dev, libcereal-dev, libedlib-dev, libspoa-dev, libthread-pool-dev (>= 3.0.2), rampler, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), cmake, libgtest-dev, libbioparser-dev, libcereal-dev, libedlib-dev, libspoa-dev, libthread-pool-dev (>= 3.0.2), rampler, 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 [428 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [510 B]
Fetched 1895 B in 0s (49.2 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base googletest groff-base intltool-debian libarchive-zip-perl
libarchive13 libbioparser-dev libbrotli1 libcereal-dev libcurl4
libdebhelper-perl libedlib-dev libedlib0 libelf1 libexpat1
libfile-stripnondeterminism-perl libgtest-dev libicu67 libjsoncpp24
libmagic-mgc libmagic1 libncurses6 libncursesw6 libnghttp2-14 libpipeline1
libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2 libspoa-dev libspoa7.0.0
libssh2-1 libsub-override-perl libthread-pool-dev libtinfo6 libtool
libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps rampler
rapidjson-dev sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make
gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl rapidjson-doc
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libgpm2 publicsuffix
libltdl-dev libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base googletest groff-base intltool-debian libarchive-zip-perl
libarchive13 libbioparser-dev libbrotli1 libcereal-dev libcurl4
libdebhelper-perl libedlib-dev libedlib0 libelf1 libexpat1
libfile-stripnondeterminism-perl libgtest-dev libicu67 libjsoncpp24
libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpipeline1 libprocps8
libpsl5 librhash0 librtmp1 libsigsegv2 libspoa-dev libspoa7.0.0 libssh2-1
libsub-override-perl libthread-pool-dev libtool libuchardet0 libuv1 libxml2
m4 man-db po-debconf procps rampler rapidjson-dev
sbuild-build-depends-main-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
libncursesw6 libtinfo6
2 upgraded, 60 newly installed, 0 to remove and 61 not upgraded.
Need to get 27.6 MB of archives.
After this operation, 112 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [936 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf libtinfo6 armhf 6.2+20201114-4 [328 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libncursesw6 armhf 6.2+20201114-4 [105 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-5 [60.5 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-5 [475 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf cmake-data all 3.18.4-2+rpi1 [1725 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [580 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.9.0-3 [151 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libcurl4 armhf 7.74.0-1.3 [305 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.2.10-2 [73.4 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libjsoncpp24 armhf 1.9.4-4 [67.0 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf librhash0 armhf 1.4.2-1 [141 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libuv1 armhf 1.40.0-2 [119 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf cmake armhf 3.18.4-2+rpi1 [3118 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.1 [192 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.1 [1056 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf googletest all 1.10.0.20201025-1.1 [629 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libbioparser-dev all 3.0.12-1 [7168 B]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf rapidjson-dev all 1.1.0+dfsg2-7 [98.9 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libcereal-dev all 1.3.0+dfsg-1 [210 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf libedlib0 armhf 1.2.6-1 [13.6 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libedlib-dev armhf 1.2.6-1 [15.9 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf libgtest-dev armhf 1.10.0.20201025-1.1 [1388 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libspoa7.0.0 armhf 4.0.7+ds-1 [51.3 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf libspoa-dev armhf 4.0.7+ds-1 [6720 B]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libthread-pool-dev all 3.0.2-1 [4376 B]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf rampler armhf 2.0.0-1 [19.1 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 12481 files and directories currently installed.)
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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.10-2) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-1) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.5.1) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up googletest (1.10.0.20201025-1.1) ...
Setting up rapidjson-dev (1.1.0+dfsg2-7) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libuv1:armhf (1.40.0-2) ...
Setting up rampler (2.0.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-4) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libthread-pool-dev (3.0.2-1) ...
Setting up libspoa7.0.0:armhf (4.0.7+ds-1) ...
Setting up autopoint (0.21-4) ...
Setting up libedlib0 (1.2.6-1) ...
Setting up libjsoncpp24:armhf (1.9.4-4) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.17) ...
Setting up libbioparser-dev (3.0.12-1) ...
Setting up librhash0:armhf (1.4.2-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.9.0-3) ...
Setting up cmake-data (3.18.4-2+rpi1) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.7) ...
Setting up libprocps8:armhf (2:3.3.17-5) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up gettext (0.21-4) ...
Setting up libgtest-dev:armhf (1.10.0.20201025-1.1) ...
Setting up libtool (2.4.6-15) ...
Setting up libarchive13:armhf (3.4.3-2) ...
Setting up libcereal-dev (1.3.0+dfsg-1) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libedlib-dev (1.2.6-1) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up procps (2:3.3.17-5) ...
Setting up libcurl4:armhf (7.74.0-1.3) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libspoa-dev:armhf (4.0.7+ds-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up cmake (3.18.4-2+rpi1) ...
Setting up debhelper (13.5.1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-13+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.35.2-2+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-13+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.2.4 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1+rpi1 base-passwd_3.5.51 bash_5.1-2 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.36.1-8 build-essential_12.9 bzip2_1.0.8-4 cmake_3.18.4-2+rpi1 cmake-data_3.18.4-2+rpi1 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.77 debhelper_13.5.1 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.2-2 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.3.0-22+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 googletest_1.10.0.20201025-1.1 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.2-2+rpi1 libbioparser-dev_3.0.12-1 libblkid1_2.36.1-8 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-13+rpi1 libc-dev-bin_2.31-13+rpi1 libc6_2.31-13+rpi1 libc6-dev_2.31-13+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcereal-dev_1.3.0+dfsg-1 libcom-err2_1.46.2-2 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libcurl4_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.1 libdpkg-perl_1.20.9+rpi1 libedlib-dev_1.2.6-1 libedlib0_1.2.6-1 libelf1_0.185-2 libexpat1_2.2.10-2 libext2fs2_1.46.2-2 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-6 libgtest-dev_1.10.0.20201025-1.1 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.0-5 libisl23_0.23-1 libjsoncpp24_1.9.4-4 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-3 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-8 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-9 libpam-modules-bin_1.4.0-9 libpam-runtime_1.4.0-9 libpam0g_1.4.0-9 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-4+deb11u1 libpipeline1_1.5.3-1 libprocps8_2:3.3.17-5 libpsl5_0.21.0-1.2 libreadline8_8.1-1 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-8 libspoa-dev_4.0.7+ds-1 libspoa7.0.0_4.0.7+ds-1 libsqlite3-0_3.34.1-3 libss2_1.46.2-2 libssh2-1_1.9.0-3 libssl1.1_1.1.1k-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-6+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libthread-pool-dev_3.0.2-1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-6+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-8 libuv1_1.40.0-2 libxml2_2.9.10+dfsg-6.7 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.2-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.36.1-8 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4+deb11u1 perl-base_5.32.1-4+deb11u1 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 procps_2:3.3.17-5 rampler_2.0.0-1 rapidjson-dev_1.1.0+dfsg2-7 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.17 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-8 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: racon
Binary: racon
Architecture: any
Version: 1.4.21-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Cédric Lood <cedric.lood@kuleuven.be>, Andreas Tille <tille@debian.org>
Homepage: https://github.com/lbcb-sci/racon
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/racon
Vcs-Git: https://salsa.debian.org/med-team/racon.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), cmake, libgtest-dev, libbioparser-dev, libcereal-dev, libedlib-dev, libspoa-dev, libthread-pool-dev (>= 3.0.2), rampler
Package-List:
racon deb science optional arch=any
Checksums-Sha1:
97603e533070b85bf283dcb98f5493198298d7d4 3083387 racon_1.4.21.orig.tar.gz
9cecd22d5daf6d69c0e39e2ed8adcaa88ec0e59e 6332 racon_1.4.21-1.debian.tar.xz
Checksums-Sha256:
be293cb26d167c5353cacba69f4c86cb6924e234c5e1902e8e4e68ed70217d66 3083387 racon_1.4.21.orig.tar.gz
6d8da43756abde566eb3f772074d566486be6c2be5e9b87355293c501f5f5668 6332 racon_1.4.21-1.debian.tar.xz
Files:
16a15e31e39046b4acf860e430307ebd 3083387 racon_1.4.21.orig.tar.gz
d108f09cfeaf2739d1b895e8d692c235 6332 racon_1.4.21-1.debian.tar.xz
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-----END PGP SIGNATURE-----
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.K65GAehG/trustedkeys.kbx': General error
gpgv: Signature made Wed Sep 1 15:27:00 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./racon_1.4.21-1.dsc
dpkg-source: info: extracting racon in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking racon_1.4.21.orig.tar.gz
dpkg-source: info: unpacking racon_1.4.21-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_libs.patch
dpkg-source: info: applying remove_buildpath
dpkg-source: info: applying py3
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=e040c44591bf400793155c77e2e04554
JOURNAL_STREAM=8:7708138
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-3169e2c3-9c18-4f42-84d9-597a788e0ef6
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c85515
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 racon
dpkg-buildpackage: info: source version 1.4.21-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --buildsystem=cmake
dh_auto_clean -O--buildsystem=cmake
dh_autoreconf_clean -O--buildsystem=cmake
dh_clean -O--buildsystem=cmake
debian/rules binary-arch
dh binary-arch --buildsystem=cmake
dh_update_autotools_config -a -O--buildsystem=cmake
dh_autoreconf -a -O--buildsystem=cmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -Dracon_build_tests=ON -Dracon_build_wrapper=ON
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 -Dracon_build_tests=ON -Dracon_build_wrapper=ON ..
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- 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
-- Found GTest: /usr/lib/arm-linux-gnueabihf/libgtest.a
-- 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
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
# Somehow the means in the patch for CMakeLists.txt to replace -lpthread by -pthread to not work
# Just hack it here
sed -i 's/-lpthread/-pthread/' obj-*/CMakeFiles/racon_test.dir/link.txt
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a -O--buildsystem=cmake
cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/<<PKGBUILDDIR>>/src/overlap.cpp:219:48: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=]
219 | "edlib unable to align pair (%zu x %zu)!\n", q_id_, t_id_);
| ~~^ ~~~~~
| | |
| unsigned int uint64_t {aka long long unsigned int}
| %llu
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219 | "edlib unable to align pair (%zu x %zu)!\n", q_id_, t_id_);
| ~~^ ~~~~~
| | |
| unsigned int uint64_t {aka long long unsigned int}
| %llu
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/<<PKGBUILDDIR>>/src/overlap.cpp:219:48: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=]
219 | "edlib unable to align pair (%zu x %zu)!\n", q_id_, t_id_);
| ~~^ ~~~~~
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| %llu
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219 | "edlib unable to align pair (%zu x %zu)!\n", q_id_, t_id_);
| ~~^ ~~~~~
| | |
| unsigned int uint64_t {aka long long unsigned int}
| %llu
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142 | "contig %lu might be chimeric in window %u!\n", id_, rank_);
| ~~^ ~~~
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142 | "contig %lu might be chimeric in window %u!\n", id_, rank_);
| ~~^ ~~~
| | |
| long unsigned int uint64_t {aka long long unsigned int}
| %llu
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Running main() from /build/googletest-MTVrzi/googletest-1.10.0.20201025/googletest/src/gtest_main.cc
[==========] Running 15 tests from 2 test suites.
[----------] Global test environment set-up.
[----------] 5 tests from RaconInitializeTest
[ RUN ] RaconInitializeTest.PolisherTypeError
[ OK ] RaconInitializeTest.PolisherTypeError (3 ms)
[ RUN ] RaconInitializeTest.WindowLengthError
[ OK ] RaconInitializeTest.WindowLengthError (3 ms)
[ RUN ] RaconInitializeTest.SequencesPathExtensionError
[ OK ] RaconInitializeTest.SequencesPathExtensionError (3 ms)
[ RUN ] RaconInitializeTest.OverlapsPathExtensionError
[ OK ] RaconInitializeTest.OverlapsPathExtensionError (12 ms)
[ RUN ] RaconInitializeTest.TargetPathExtensionError
[ OK ] RaconInitializeTest.TargetPathExtensionError (14 ms)
[----------] 5 tests from RaconInitializeTest (35 ms total)
[----------] 10 tests from RaconPolishingTest
[ RUN ] RaconPolishingTest.ConsensusWithQualities
[racon::Polisher::initialize] loaded target sequences 0.001890 s
[racon::Polisher::initialize] loaded sequences 0.125408 s
[racon::Polisher::initialize] loaded overlaps 0.001341 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.085059 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.143235 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.176036 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.237906 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.280518 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.316162 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.384639 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.446210 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.493312 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.552404 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.598401 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.655779 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.732487 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.776016 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.840694 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.905478 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.952458 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 1.006287 s
[racon::Polisher::initialize] aligning overlaps [===================>] 1.071078 s
[racon::Polisher::initialize] aligning overlaps [====================] 1.155581 s
[racon::Polisher::initialize] transformed data into windows 0.005174 s
[racon::Polisher::polish] generating consensus [=> ] 0.532264 s
[racon::Polisher::polish] generating consensus [==> ] 1.033717 s
[racon::Polisher::polish] generating consensus [===> ] 1.414986 s
[racon::Polisher::polish] generating consensus [====> ] 1.735277 s
[racon::Polisher::polish] generating consensus [=====> ] 2.009370 s
[racon::Polisher::polish] generating consensus [======> ] 2.147405 s
[racon::Polisher::polish] generating consensus [=======> ] 2.339840 s
[racon::Polisher::polish] generating consensus [========> ] 2.713401 s
[racon::Polisher::polish] generating consensus [=========> ] 3.133128 s
[racon::Polisher::polish] generating consensus [==========> ] 3.620427 s
[racon::Polisher::polish] generating consensus [===========> ] 4.411193 s
[racon::Polisher::polish] generating consensus [============> ] 5.256980 s
[racon::Polisher::polish] generating consensus [=============> ] 6.320053 s
[racon::Polisher::polish] generating consensus [==============> ] 7.740401 s
[racon::Polisher::polish] generating consensus [===============> ] 8.518212 s
[racon::Polisher::polish] generating consensus [================> ] 9.335746 s
[racon::Polisher::polish] generating consensus [=================> ] 10.278189 s
[racon::Polisher::polish] generating consensus [==================> ] 10.896380 s
[racon::Polisher::polish] generating consensus [===================>] 11.538461 s
[racon::Polisher::polish] generating consensus [====================] 14.726081 s
[racon::Polisher::] total = 16.079529 s
[ OK ] RaconPolishingTest.ConsensusWithQualities (16106 ms)
[ RUN ] RaconPolishingTest.ConsensusWithoutQualities
[racon::Polisher::initialize] loaded target sequences 0.001569 s
[racon::Polisher::initialize] loaded sequences 0.062718 s
[racon::Polisher::initialize] loaded overlaps 0.001418 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.084362 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.138963 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.185546 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.272794 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.341122 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.385562 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.476960 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.551966 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.614402 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.711305 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.784636 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.872931 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.973742 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 1.031936 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 1.136936 s
[racon::Polisher::initialize] aligning overlaps [================> ] 1.225158 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 1.287432 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 1.358848 s
[racon::Polisher::initialize] aligning overlaps [===================>] 1.442438 s
[racon::Polisher::initialize] aligning overlaps [====================] 1.555433 s
[racon::Polisher::initialize] transformed data into windows 0.001755 s
[racon::Polisher::polish] generating consensus [=> ] 0.731911 s
[racon::Polisher::polish] generating consensus [==> ] 1.672252 s
[racon::Polisher::polish] generating consensus [===> ] 2.376799 s
[racon::Polisher::polish] generating consensus [====> ] 2.889467 s
[racon::Polisher::polish] generating consensus [=====> ] 3.233214 s
[racon::Polisher::polish] generating consensus [======> ] 3.624851 s
[racon::Polisher::polish] generating consensus [=======> ] 4.073558 s
[racon::Polisher::polish] generating consensus [========> ] 4.677652 s
[racon::Polisher::polish] generating consensus [=========> ] 5.344703 s
[racon::Polisher::polish] generating consensus [==========> ] 6.320469 s
[racon::Polisher::polish] generating consensus [===========> ] 7.373126 s
[racon::Polisher::polish] generating consensus [============> ] 8.657378 s
[racon::Polisher::polish] generating consensus [=============> ] 10.514354 s
[racon::Polisher::polish] generating consensus [==============> ] 11.902334 s
[racon::Polisher::polish] generating consensus [===============> ] 13.273215 s
[racon::Polisher::polish] generating consensus [================> ] 14.411868 s
[racon::Polisher::polish] generating consensus [=================> ] 15.587738 s
[racon::Polisher::polish] generating consensus [==================> ] 16.264965 s
[racon::Polisher::polish] generating consensus [===================>] 17.314291 s
[racon::Polisher::polish] generating consensus [====================] 22.740000 s
[racon::Polisher::] total = 24.461650 s
[ OK ] RaconPolishingTest.ConsensusWithoutQualities (24490 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments
[racon::Polisher::initialize] loaded target sequences 0.002541 s
[racon::Polisher::initialize] loaded sequences 0.169218 s
[racon::Polisher::initialize] loaded overlaps 0.105657 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.026979 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.027753 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.028406 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.029040 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.029659 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.030276 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.030889 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.031501 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.032113 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.032724 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.033336 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.033948 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.034558 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.035171 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.035781 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.036456 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.037085 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.037694 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.038305 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.038921 s
[racon::Polisher::initialize] transformed data into windows 0.004975 s
[racon::Polisher::polish] generating consensus [=> ] 0.718338 s
[racon::Polisher::polish] generating consensus [==> ] 1.457849 s
[racon::Polisher::polish] generating consensus [===> ] 2.036232 s
[racon::Polisher::polish] generating consensus [====> ] 2.534350 s
[racon::Polisher::polish] generating consensus [=====> ] 2.802226 s
[racon::Polisher::polish] generating consensus [======> ] 3.056605 s
[racon::Polisher::polish] generating consensus [=======> ] 3.321265 s
[racon::Polisher::polish] generating consensus [========> ] 3.747553 s
[racon::Polisher::polish] generating consensus [=========> ] 4.113816 s
[racon::Polisher::polish] generating consensus [==========> ] 4.795710 s
[racon::Polisher::polish] generating consensus [===========> ] 5.671827 s
[racon::Polisher::polish] generating consensus [============> ] 6.688160 s
[racon::Polisher::polish] generating consensus [=============> ] 8.184335 s
[racon::Polisher::polish] generating consensus [==============> ] 9.719466 s
[racon::Polisher::polish] generating consensus [===============> ] 10.629440 s
[racon::Polisher::polish] generating consensus [================> ] 11.462142 s
[racon::Polisher::polish] generating consensus [=================> ] 12.406651 s
[racon::Polisher::polish] generating consensus [==================> ] 13.034446 s
[racon::Polisher::polish] generating consensus [===================>] 13.707195 s
[racon::Polisher::polish] generating consensus [====================] 17.131292 s
[racon::Polisher::] total = 17.535592 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments (17575 ms)
[ RUN ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments
[racon::Polisher::initialize] loaded target sequences 0.002051 s
[racon::Polisher::initialize] loaded sequences 0.063516 s
[racon::Polisher::initialize] loaded overlaps 0.113883 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.014516 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.015426 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.016179 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.016911 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.017548 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.018341 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.019136 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.019813 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.020514 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.021255 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.022080 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.023022 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.023975 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.024810 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.025552 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.029585 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.030035 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.030471 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.030902 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.031333 s
[racon::Polisher::initialize] transformed data into windows 0.001740 s
[racon::Polisher::polish] generating consensus [=> ] 0.770602 s
[racon::Polisher::polish] generating consensus [==> ] 1.731593 s
[racon::Polisher::polish] generating consensus [===> ] 2.508211 s
[racon::Polisher::polish] generating consensus [====> ] 3.002263 s
[racon::Polisher::polish] generating consensus [=====> ] 3.404016 s
[racon::Polisher::polish] generating consensus [======> ] 3.820139 s
[racon::Polisher::polish] generating consensus [=======> ] 4.280452 s
[racon::Polisher::polish] generating consensus [========> ] 4.945025 s
[racon::Polisher::polish] generating consensus [=========> ] 5.456118 s
[racon::Polisher::polish] generating consensus [==========> ] 6.412949 s
[racon::Polisher::polish] generating consensus [===========> ] 7.461739 s
[racon::Polisher::polish] generating consensus [============> ] 8.795180 s
[racon::Polisher::polish] generating consensus [=============> ] 10.874835 s
[racon::Polisher::polish] generating consensus [==============> ] 12.512826 s
[racon::Polisher::polish] generating consensus [===============> ] 13.935488 s
[racon::Polisher::polish] generating consensus [================> ] 15.240622 s
[racon::Polisher::polish] generating consensus [=================> ] 16.510037 s
[racon::Polisher::polish] generating consensus [==================> ] 17.118834 s
[racon::Polisher::polish] generating consensus [===================>] 17.862956 s
[racon::Polisher::polish] generating consensus [====================] 22.955592 s
[racon::Polisher::] total = 23.233774 s
[ OK ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments (23268 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow
[racon::Polisher::initialize] loaded target sequences 0.002058 s
[racon::Polisher::initialize] loaded sequences 0.155584 s
[racon::Polisher::initialize] loaded overlaps 0.001418 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.102148 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.174726 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.224947 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.321523 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.384055 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.431765 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.539595 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.646012 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.704210 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.802148 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.872285 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.950185 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 1.051416 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 1.120512 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 1.243253 s
[racon::Polisher::initialize] aligning overlaps [================> ] 1.355015 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 1.431942 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 1.518817 s
[racon::Polisher::initialize] aligning overlaps [===================>] 1.612162 s
[racon::Polisher::initialize] aligning overlaps [====================] 1.769785 s
[racon::Polisher::initialize] transformed data into windows 0.007562 s
[racon::Polisher::polish] generating consensus [=> ] 3.203361 s
[racon::Polisher::polish] generating consensus [==> ] 3.204050 s
[racon::Polisher::polish] generating consensus [===> ] 5.703007 s
[racon::Polisher::polish] generating consensus [====> ] 5.703588 s
[racon::Polisher::polish] generating consensus [=====> ] 6.566209 s
[racon::Polisher::polish] generating consensus [======> ] 6.962968 s
[racon::Polisher::polish] generating consensus [=======> ] 7.560542 s
[racon::Polisher::polish] generating consensus [========> ] 8.641495 s
[racon::Polisher::polish] generating consensus [=========> ] 9.686478 s
[racon::Polisher::polish] generating consensus [==========> ] 11.494590 s
[racon::Polisher::polish] generating consensus [===========> ] 13.603890 s
[racon::Polisher::polish] generating consensus [============> ] 15.622946 s
[racon::Polisher::polish] generating consensus [=============> ] 19.461508 s
[racon::Polisher::polish] generating consensus [==============> ] 21.414507 s
[racon::Polisher::polish] generating consensus [===============> ] 23.404581 s
[racon::Polisher::polish] generating consensus [================> ] 24.907308 s
[racon::Polisher::polish] generating consensus [=================> ] 27.102700 s
[racon::Polisher::polish] generating consensus [==================> ] 27.926340 s
[racon::Polisher::polish] generating consensus [===================>] 29.893148 s
[racon::Polisher::polish] generating consensus [====================] 36.812954 s
[racon::Polisher::] total = 38.838698 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow (38879 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesEditDistance
[racon::Polisher::initialize] loaded target sequences 0.002051 s
[racon::Polisher::initialize] loaded sequences 0.155806 s
[racon::Polisher::initialize] loaded overlaps 0.001428 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.113380 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.209334 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.261530 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.357750 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.427975 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.486898 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.612153 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.692023 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.772444 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.873125 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.938932 s
[racon::Polisher::initialize] aligning overlaps [============> ] 1.032990 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 1.186575 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 1.251667 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 1.363132 s
[racon::Polisher::initialize] aligning overlaps [================> ] 1.455945 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 1.529735 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 1.624287 s
[racon::Polisher::initialize] aligning overlaps [===================>] 1.719520 s
[racon::Polisher::initialize] aligning overlaps [====================] 1.857433 s
[racon::Polisher::initialize] transformed data into windows 0.006867 s
[racon::Polisher::polish] generating consensus [=> ] 0.864189 s
[racon::Polisher::polish] generating consensus [==> ] 1.654357 s
[racon::Polisher::polish] generating consensus [===> ] 2.245802 s
[racon::Polisher::polish] generating consensus [====> ] 2.732679 s
[racon::Polisher::polish] generating consensus [=====> ] 3.098836 s
[racon::Polisher::polish] generating consensus [======> ] 3.305916 s
[racon::Polisher::polish] generating consensus [=======> ] 3.626674 s
[racon::Polisher::polish] generating consensus [========> ] 4.120591 s
[racon::Polisher::polish] generating consensus [=========> ] 4.700821 s
[racon::Polisher::polish] generating consensus [==========> ] 5.308522 s
[racon::Polisher::polish] generating consensus [===========> ] 6.396397 s
[racon::Polisher::polish] generating consensus [============> ] 8.207818 s
[racon::Polisher::polish] generating consensus [=============> ] 10.236847 s
[racon::Polisher::polish] generating consensus [==============> ] 12.204752 s
[racon::Polisher::polish] generating consensus [===============> ] 12.906735 s
[racon::Polisher::polish] generating consensus [================> ] 13.826009 s
[racon::Polisher::polish] generating consensus [=================> ] 14.767241 s
[racon::Polisher::polish] generating consensus [==================> ] 15.550004 s
[racon::Polisher::polish] generating consensus [===================>] 16.293897 s
[racon::Polisher::polish] generating consensus [====================] 20.109742 s
[racon::Polisher::] total = 22.230275 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesEditDistance (22264 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualities
[racon::Polisher::initialize] loaded target sequences 0.155984 s
[racon::Polisher::initialize] loaded sequences 0.164043 s
[racon::Polisher::initialize] loaded overlaps 0.044425 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.113618 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.187714 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.288246 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.343774 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.418900 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.467271 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.560085 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.595627 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.691843 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.819031 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.896889 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.995582 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 1.147606 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 1.263568 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 1.389796 s
[racon::Polisher::initialize] aligning overlaps [================> ] 1.508450 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 1.597138 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 1.775491 s
[racon::Polisher::initialize] aligning overlaps [===================>] 1.874225 s
[racon::Polisher::initialize] aligning overlaps [====================] 2.173663 s
[racon::Polisher::initialize] transformed data into windows 0.017208 s
[racon::Polisher::polish] generating consensus [=> ] 0.564598 s
[racon::Polisher::polish] generating consensus [==> ] 1.185457 s
[racon::Polisher::polish] generating consensus [===> ] 1.765422 s
[racon::Polisher::polish] generating consensus [====> ] 1.766730 s
[racon::Polisher::polish] generating consensus [=====> ] 2.253612 s
[racon::Polisher::polish] generating consensus [======> ] 2.544361 s
[racon::Polisher::polish] generating consensus [=======> ] 2.960839 s
[racon::Polisher::polish] generating consensus [========> ] 2.999807 s
[racon::Polisher::polish] generating consensus [=========> ] 3.935439 s
[racon::Polisher::polish] generating consensus [==========> ] 4.294585 s
[racon::Polisher::polish] generating consensus [===========> ] 4.567518 s
[racon::Polisher::polish] generating consensus [============> ] 4.667246 s
[racon::Polisher::polish] generating consensus [=============> ] 5.035903 s
[racon::Polisher::polish] generating consensus [==============> ] 5.036731 s
[racon::Polisher::polish] generating consensus [===============> ] 5.863764 s
[racon::Polisher::polish] generating consensus [================> ] 5.864475 s
[racon::Polisher::polish] generating consensus [=================> ] 7.429711 s
[racon::Polisher::polish] generating consensus [==================> ] 7.986146 s
[racon::Polisher::polish] generating consensus [===================>] 8.684299 s
[racon::Polisher::polish] generating consensus [====================] 9.005778 s
[racon::Polisher::] total = 11.566153 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualities (11599 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull
[racon::Polisher::initialize] loaded target sequences 0.211069 s
[racon::Polisher::initialize] loaded sequences 0.175395 s
[racon::Polisher::initialize] loaded overlaps 0.054051 s
[racon::Polisher::initialize] aligning overlaps [=> ] 2.478846 s
[racon::Polisher::initialize] aligning overlaps [==> ] 4.224424 s
[racon::Polisher::initialize] aligning overlaps [===> ] 5.775414 s
[racon::Polisher::initialize] aligning overlaps [====> ] 7.892380 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 9.487084 s
[racon::Polisher::initialize] aligning overlaps [======> ] 10.919715 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 12.849837 s
[racon::Polisher::initialize] aligning overlaps [========> ] 15.156888 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 17.522612 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 19.639705 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 21.275216 s
[racon::Polisher::initialize] aligning overlaps [============> ] 23.694603 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 26.260934 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 28.399061 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 31.045620 s
[racon::Polisher::initialize] aligning overlaps [================> ] 33.581804 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 35.862591 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 38.325107 s
[racon::Polisher::initialize] aligning overlaps [===================>] 40.924149 s
[racon::Polisher::initialize] aligning overlaps [====================] 43.405862 s
[racon::Polisher::initialize] transformed data into windows 0.232581 s
[racon::Polisher::polish] generating consensus [=> ] 31.671973 s
[racon::Polisher::polish] generating consensus [==> ] 54.613962 s
[racon::Polisher::polish] generating consensus [===> ] 81.221118 s
[racon::Polisher::polish] generating consensus [====> ] 102.765918 s
[racon::Polisher::polish] generating consensus [=====> ] 127.683460 s
[racon::Polisher::polish] generating consensus [======> ] 155.743527 s
[racon::Polisher::polish] generating consensus [=======> ] 183.478811 s
[racon::Polisher::polish] generating consensus [========> ] 204.988092 s
[racon::Polisher::polish] generating consensus [=========> ] 232.073963 s
[racon::Polisher::polish] generating consensus [==========> ] 264.446442 s
[racon::Polisher::polish] generating consensus [===========> ] 291.683793 s
[racon::Polisher::polish] generating consensus [============> ] 322.548019 s
[racon::Polisher::polish] generating consensus [=============> ] 349.459494 s
[racon::Polisher::polish] generating consensus [==============> ] 378.783770 s
[racon::Polisher::polish] generating consensus [===============> ] 409.256852 s
[racon::Polisher::polish] generating consensus [================> ] 427.648796 s
[racon::Polisher::polish] generating consensus [=================> ] 460.151500 s
[racon::Polisher::polish] generating consensus [==================> ] 490.890132 s
[racon::Polisher::polish] generating consensus [===================>] 521.259551 s
[racon::Polisher::polish] generating consensus [====================] 550.259145 s
[racon::Polisher::] total = 594.349902 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull (594391 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull
[racon::Polisher::initialize] loaded target sequences 0.079108 s
[racon::Polisher::initialize] loaded sequences 0.079499 s
[racon::Polisher::initialize] loaded overlaps 0.054096 s
[racon::Polisher::initialize] aligning overlaps [=> ] 2.757365 s
[racon::Polisher::initialize] aligning overlaps [==> ] 4.626868 s
[racon::Polisher::initialize] aligning overlaps [===> ] 6.193909 s
[racon::Polisher::initialize] aligning overlaps [====> ] 8.451583 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 10.277732 s
[racon::Polisher::initialize] aligning overlaps [======> ] 11.831810 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 13.828717 s
[racon::Polisher::initialize] aligning overlaps [========> ] 16.133304 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 18.557580 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 20.759330 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 22.598207 s
[racon::Polisher::initialize] aligning overlaps [============> ] 25.114288 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 27.819793 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 30.176749 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 32.843499 s
[racon::Polisher::initialize] aligning overlaps [================> ] 35.581971 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 38.037338 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 40.685896 s
[racon::Polisher::initialize] aligning overlaps [===================>] 43.450422 s
[racon::Polisher::initialize] aligning overlaps [====================] 45.978323 s
[racon::Polisher::initialize] transformed data into windows 0.061747 s
[racon::Polisher::polish] generating consensus [=> ] 47.551267 s
[racon::Polisher::polish] generating consensus [==> ] 84.002604 s
[racon::Polisher::polish] generating consensus [===> ] 123.091055 s
[racon::Polisher::polish] generating consensus [====> ] 152.559189 s
[racon::Polisher::polish] generating consensus [=====> ] 188.821787 s
[racon::Polisher::polish] generating consensus [======> ] 228.505733 s
[racon::Polisher::polish] generating consensus [=======> ] 272.368963 s
[racon::Polisher::polish] generating consensus [========> ] 303.859514 s
[racon::Polisher::polish] generating consensus [=========> ] 342.215409 s
[racon::Polisher::polish] generating consensus [==========> ] 388.475180 s
[racon::Polisher::polish] generating consensus [===========> ] 428.069024 s
[racon::Polisher::polish] generating consensus [============> ] 470.539571 s
[racon::Polisher::polish] generating consensus [=============> ] 510.647539 s
[racon::Polisher::polish] generating consensus [==============> ] 551.907153 s
[racon::Polisher::polish] generating consensus [===============> ] 593.518696 s
[racon::Polisher::polish] generating consensus [================> ] 616.239046 s
[racon::Polisher::polish] generating consensus [=================> ] 667.198977 s
[racon::Polisher::polish] generating consensus [==================> ] 714.466428 s
[racon::Polisher::polish] generating consensus [===================>] 758.997156 s
[racon::Polisher::polish] generating consensus [====================] 799.002134 s
[racon::Polisher::] total = 845.263440 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull (845307 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap
[racon::Polisher::initialize] loaded target sequences 0.174371 s
[racon::Polisher::initialize] loaded sequences 0.171046 s
[racon::Polisher::initialize] loaded overlaps 0.054707 s
[racon::Polisher::initialize] aligning overlaps [=> ] 2.519247 s
[racon::Polisher::initialize] aligning overlaps [==> ] 4.297446 s
[racon::Polisher::initialize] aligning overlaps [===> ] 5.939423 s
[racon::Polisher::initialize] aligning overlaps [====> ] 8.241801 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 10.097732 s
[racon::Polisher::initialize] aligning overlaps [======> ] 11.564361 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 13.610040 s
[racon::Polisher::initialize] aligning overlaps [========> ] 16.034360 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 18.497785 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 20.749468 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 22.499628 s
[racon::Polisher::initialize] aligning overlaps [============> ] 25.053732 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 27.707184 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 30.092621 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 32.841818 s
[racon::Polisher::initialize] aligning overlaps [================> ] 35.574658 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 38.095641 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 40.798720 s
[racon::Polisher::initialize] aligning overlaps [===================>] 43.620971 s
[racon::Polisher::initialize] aligning overlaps [====================] 46.181065 s
[racon::Polisher::initialize] transformed data into windows 0.249540 s
[racon::Polisher::polish] generating consensus [=> ] 34.556878 s
[racon::Polisher::polish] generating consensus [==> ] 58.971323 s
[racon::Polisher::polish] generating consensus [===> ] 86.814077 s
[racon::Polisher::polish] generating consensus [====> ] 110.096541 s
[racon::Polisher::polish] generating consensus [=====> ] 136.579749 s
[racon::Polisher::polish] generating consensus [======> ] 166.332166 s
[racon::Polisher::polish] generating consensus [=======> ] 196.873870 s
[racon::Polisher::polish] generating consensus [========> ] 219.726745 s
[racon::Polisher::polish] generating consensus [=========> ] 247.924647 s
[racon::Polisher::polish] generating consensus [==========> ] 281.507252 s
[racon::Polisher::polish] generating consensus [===========> ] 311.346800 s
[racon::Polisher::polish] generating consensus [============> ] 342.652892 s
[racon::Polisher::polish] generating consensus [=============> ] 370.073207 s
[racon::Polisher::polish] generating consensus [==============> ] 400.285471 s
[racon::Polisher::polish] generating consensus [===============> ] 431.687060 s
[racon::Polisher::polish] generating consensus [================> ] 449.990757 s
[racon::Polisher::polish] generating consensus [=================> ] 484.304406 s
[racon::Polisher::polish] generating consensus [==================> ] 516.093750 s
[racon::Polisher::polish] generating consensus [===================>] 547.124863 s
[racon::Polisher::polish] generating consensus [====================] 576.692506 s
[racon::Polisher::] total = 623.535168 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap (623583 ms)
[----------] 10 tests from RaconPolishingTest (2217467 ms total)
[----------] Global test environment tear-down
[==========] 15 tests from 2 test suites ran. (2217503 ms total)
[ PASSED ] 15 tests.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=cmake
dh_prep -a -O--buildsystem=cmake
dh_auto_install --destdir=debian/racon/ -a -O--buildsystem=cmake
cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/racon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: 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
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<PKGBUILDDIR>>/debian/racon/usr/bin/racon
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
dh_install -a -O--buildsystem=cmake
dh_installdocs -a -O--buildsystem=cmake
dh_installchangelogs -a -O--buildsystem=cmake
dh_installexamples -a -O--buildsystem=cmake
dh_installman -a -O--buildsystem=cmake
dh_installsystemduser -a -O--buildsystem=cmake
dh_lintian -a -O--buildsystem=cmake
dh_perl -a -O--buildsystem=cmake
dh_link -a -O--buildsystem=cmake
dh_strip_nondeterminism -a -O--buildsystem=cmake
dh_compress -a -O--buildsystem=cmake
dh_fixperms -a -O--buildsystem=cmake
dh_missing -a -O--buildsystem=cmake
dh_dwz -a -a -O--buildsystem=cmake
dh_strip -a -a -O--buildsystem=cmake
dh_makeshlibs -a -a -O--buildsystem=cmake
dh_shlibdeps -a -a -O--buildsystem=cmake
dpkg-shlibdeps: warning: debian/racon/usr/lib/racon/racon_test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/racon/usr/bin/racon contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/racon/usr/lib/racon/racon_test debian/racon/usr/bin/racon were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a -O--buildsystem=cmake
dh_gencontrol -a -O--buildsystem=cmake
dh_md5sums -a -O--buildsystem=cmake
dh_builddeb -a -O--buildsystem=cmake
dpkg-deb: building package 'racon' in '../racon_1.4.21-1_armhf.deb'.
dpkg-deb: building package 'racon-dbgsym' in '../racon-dbgsym_1.4.21-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> >../racon_1.4.21-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-09-04T08:10:19Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
racon_1.4.21-1_armhf.changes:
-----------------------------
Format: 1.8
Date: Wed, 01 Sep 2021 17:17:28 +0200
Source: racon
Binary: racon racon-dbgsym
Architecture: armhf
Version: 1.4.21-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
racon - consensus module for raw de novo DNA assembly of long uncorrected
Changes:
racon (1.4.21-1) unstable; urgency=medium
.
* Fix watchfile to detect new versions on github (routine-update)
* New upstream version
* Standards-Version: 4.6.0 (routine-update)
* Remove constraints unnecessary since buster:
+ Build-Depends: Drop versioned constraint on libbioparser-dev.
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Files:
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a3d73538264de2f5911080ab916d0901 5976 science optional racon_1.4.21-1_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: racon
Binary: racon racon-dbgsym
Architecture: armhf
Version: 1.4.21-1
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sat, 04 Sep 2021 08:10:17 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.69-14),
automake (= 1:1.16.3-2),
autopoint (= 0.21-4),
autotools-dev (= 20180224.1+nmu1),
base-files (= 11.1+rpi1),
base-passwd (= 3.5.51),
bash (= 5.1-2),
binutils (= 2.35.2-2+rpi1),
binutils-arm-linux-gnueabihf (= 2.35.2-2+rpi1),
binutils-common (= 2.35.2-2+rpi1),
bsdextrautils (= 2.37.2-1),
bsdutils (= 1:2.36.1-8),
build-essential (= 12.9),
bzip2 (= 1.0.8-4),
cmake (= 3.18.4-2+rpi1),
cmake-data (= 3.18.4-2+rpi1),
coreutils (= 8.32-4),
cpp (= 4:10.2.1-1+rpi1),
cpp-10 (= 10.2.1-6+rpi1),
dash (= 0.5.11+git20200708+dd9ef66-5),
debconf (= 1.5.77),
debhelper (= 13.5.1),
debianutils (= 4.11.2),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.12.0-1),
diffutils (= 1:3.7-5),
dpkg (= 1.20.9+rpi1),
dpkg-dev (= 1.20.9+rpi1),
dwz (= 0.14-1),
file (= 1:5.39-3),
findutils (= 4.8.0-1),
g++ (= 4:10.2.1-1+rpi1),
g++-10 (= 10.2.1-6+rpi1),
gcc (= 4:10.2.1-1+rpi1),
gcc-10 (= 10.2.1-6+rpi1),
gcc-10-base (= 10.2.1-6+rpi1),
gettext (= 0.21-4),
gettext-base (= 0.21-4),
googletest (= 1.10.0.20201025-1.1),
grep (= 3.6-1),
groff-base (= 1.22.4-6),
gzip (= 1.10-4),
hostname (= 3.23),
init-system-helpers (= 1.60),
intltool-debian (= 0.35.0+20060710.5),
libacl1 (= 2.2.53-10),
libarchive-zip-perl (= 1.68-1),
libarchive13 (= 3.4.3-2),
libasan6 (= 10.2.1-6+rpi1),
libatomic1 (= 10.2.1-6+rpi1),
libattr1 (= 1:2.4.48-6),
libaudit-common (= 1:3.0-2),
libaudit1 (= 1:3.0-2),
libbinutils (= 2.35.2-2+rpi1),
libbioparser-dev (= 3.0.12-1),
libblkid1 (= 2.36.1-8),
libbrotli1 (= 1.0.9-2+b1),
libbz2-1.0 (= 1.0.8-4),
libc-bin (= 2.31-13+rpi1),
libc-dev-bin (= 2.31-13+rpi1),
libc6 (= 2.31-13+rpi1),
libc6-dev (= 2.31-13+rpi1),
libcap-ng0 (= 0.7.9-2.2+b1),
libcc1-0 (= 10.2.1-6+rpi1),
libcereal-dev (= 1.3.0+dfsg-1),
libcom-err2 (= 1.46.2-2),
libcrypt-dev (= 1:4.4.18-4),
libcrypt1 (= 1:4.4.18-4),
libctf-nobfd0 (= 2.35.2-2+rpi1),
libctf0 (= 2.35.2-2+rpi1),
libcurl4 (= 7.74.0-1.3),
libdb5.3 (= 5.3.28+dfsg1-0.8),
libdebconfclient0 (= 0.260),
libdebhelper-perl (= 13.5.1),
libdpkg-perl (= 1.20.9+rpi1),
libedlib-dev (= 1.2.6-1),
libedlib0 (= 1.2.6-1),
libelf1 (= 0.185-2),
libexpat1 (= 2.2.10-2),
libffi7 (= 3.3-6),
libfile-stripnondeterminism-perl (= 1.12.0-1),
libgcc-10-dev (= 10.2.1-6+rpi1),
libgcc-s1 (= 10.2.1-6+rpi1),
libgcrypt20 (= 1.8.7-6),
libgdbm-compat4 (= 1.19-2),
libgdbm6 (= 1.19-2),
libgmp10 (= 2:6.2.1+dfsg-1),
libgnutls30 (= 3.7.1-5),
libgomp1 (= 10.2.1-6+rpi1),
libgpg-error0 (= 1.38-2),
libgssapi-krb5-2 (= 1.18.3-6),
libgtest-dev (= 1.10.0.20201025-1.1),
libhogweed6 (= 3.7.3-1),
libicu67 (= 67.1-7),
libidn2-0 (= 2.3.0-5),
libisl23 (= 0.23-1),
libjsoncpp24 (= 1.9.4-4),
libk5crypto3 (= 1.18.3-6),
libkeyutils1 (= 1.6.1-2),
libkrb5-3 (= 1.18.3-6),
libkrb5support0 (= 1.18.3-6),
libldap-2.4-2 (= 2.4.57+dfsg-3),
liblz4-1 (= 1.9.3-2),
liblzma5 (= 5.2.5-2),
libmagic-mgc (= 1:5.39-3),
libmagic1 (= 1:5.39-3),
libmount1 (= 2.36.1-8),
libmpc3 (= 1.2.0-1),
libmpfr6 (= 4.1.0-3),
libncurses6 (= 6.2+20201114-4),
libncursesw6 (= 6.2+20201114-4),
libnettle8 (= 3.7.3-1),
libnghttp2-14 (= 1.43.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.23.22-1),
libpam-modules (= 1.4.0-9),
libpam-modules-bin (= 1.4.0-9),
libpam-runtime (= 1.4.0-9),
libpam0g (= 1.4.0-9),
libpcre2-8-0 (= 10.36-2),
libpcre3 (= 2:8.39-13),
libperl5.32 (= 5.32.1-4+deb11u1),
libpipeline1 (= 1.5.3-1),
libprocps8 (= 2:3.3.17-5),
libpsl5 (= 0.21.0-1.2),
librhash0 (= 1.4.2-1),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.27+dfsg-2.1),
libsasl2-modules-db (= 2.1.27+dfsg-2.1),
libseccomp2 (= 2.5.1-1+rpi1),
libselinux1 (= 3.1-3),
libsigsegv2 (= 2.13-1),
libsmartcols1 (= 2.36.1-8),
libspoa-dev (= 4.0.7+ds-1),
libspoa7.0.0 (= 4.0.7+ds-1),
libssh2-1 (= 1.9.0-3),
libssl1.1 (= 1.1.1k-1),
libstdc++-10-dev (= 10.2.1-6+rpi1),
libstdc++6 (= 10.2.1-6+rpi1),
libsub-override-perl (= 0.09-2),
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libtirpc-common (= 1.3.1-1),
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libtool (= 2.4.6-15),
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libuchardet0 (= 0.0.7-1),
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libunistring2 (= 0.9.10-4),
libuuid1 (= 2.36.1-8),
libuv1 (= 1.40.0-2),
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libzstd1 (= 1.4.8+dfsg-2.1+rpi1),
linux-libc-dev (= 5.10.46-4+rpi1),
login (= 1:4.8.1-1),
lsb-base (= 11.1.0+rpi1),
m4 (= 1.4.18-5),
make (= 4.3-4.1),
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ncurses-base (= 6.2+20201114-2),
ncurses-bin (= 6.2+20201114-2),
patch (= 2.7.6-7),
perl (= 5.32.1-4+deb11u1),
perl-base (= 5.32.1-4+deb11u1),
perl-modules-5.32 (= 5.32.1-5),
po-debconf (= 1.0.21+nmu1),
procps (= 2:3.3.17-5),
rampler (= 2.0.0-1),
rapidjson-dev (= 1.1.0+dfsg2-7),
sed (= 4.7-1),
sensible-utils (= 0.0.17),
sysvinit-utils (= 2.96-7),
tar (= 1.34+dfsg-1),
util-linux (= 2.36.1-8),
xz-utils (= 5.2.5-2),
zlib1g (= 1:1.2.11.dfsg-2),
zlib1g-dev (= 1:1.2.11.dfsg-2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1630509448"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
racon-dbgsym_1.4.21-1_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 3219744 bytes: control archive=640 bytes.
406 bytes, 12 lines control
297 bytes, 3 lines md5sums
Package: racon-dbgsym
Source: racon
Version: 1.4.21-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3438
Depends: racon (= 1.4.21-1)
Section: debug
Priority: optional
Description: debug symbols for racon
Build-Ids: 35b1f96d32c8b4c1c49ff49b4a08c03970e136b4 f23d297de53db49fcdce7f575d51dafd8b9a36ff
drwxr-xr-x root/root 0 2021-09-01 15:17 ./
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/lib/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/lib/debug/.build-id/35/
-rw-r--r-- root/root 2403144 2021-09-01 15:17 ./usr/lib/debug/.build-id/35/b1f96d32c8b4c1c49ff49b4a08c03970e136b4.debug
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/lib/debug/.build-id/f2/
-rw-r--r-- root/root 781248 2021-09-01 15:17 ./usr/lib/debug/.build-id/f2/3d297de53db49fcdce7f575d51dafd8b9a36ff.debug
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 321732 2021-09-01 15:17 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/racon.debug
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/share/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-09-01 15:17 ./usr/share/doc/racon-dbgsym -> racon
racon_1.4.21-1_armhf.deb
------------------------
new Debian package, version 2.0.
size 3236248 bytes: control archive=1820 bytes.
2116 bytes, 41 lines control
1174 bytes, 15 lines md5sums
Package: racon
Version: 1.4.21-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3694
Depends: libc6 (>= 2.28), libedlib0 (>= 1.2.3), libgcc-s1 (>= 3.5), libspoa7.0.0 (>= 4.0.7+ds), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4)
Recommends: python3, rampler
Section: science
Priority: optional
Homepage: https://github.com/lbcb-sci/racon
Description: consensus module for raw de novo DNA assembly of long uncorrected reads
Racon is intended as a standalone consensus module to correct raw
contigs generated by rapid assembly methods which do not include a
consensus step. The goal of Racon is to generate genomic consensus which
is of similar or better quality compared to the output generated by
assembly methods which employ both error correction and consensus steps,
while providing a speedup of several times compared to those methods. It
supports data produced by both Pacific Biosciences and Oxford Nanopore
Technologies.
.
Racon can be used as a polishing tool after the assembly with either
Illumina data or data produced by third generation of sequencing. The
type of data inputed is automatically detected.
.
Racon takes as input only three files: contigs in FASTA/FASTQ format,
reads in FASTA/FASTQ format and overlaps/alignments between the reads
and the contigs in MHAP/PAF/SAM format. Output is a set of polished
contigs in FASTA format printed to stdout. All input files can be
compressed with gzip.
.
Racon can also be used as a read error-correction tool. In this
scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps
between reads including dual overlaps.
.
A wrapper script is also available to enable easier usage to the end-
user for large datasets. It has the same interface as racon but adds
two additional features from the outside. Sequences can be subsampled
to decrease the total execution time (accuracy might be lower) while
target sequences can be split into smaller chunks and run sequentially
to decrease memory consumption. Both features can be run at the same
time as well.
drwxr-xr-x root/root 0 2021-09-01 15:17 ./
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/bin/
-rwxr-xr-x root/root 149340 2021-09-01 15:17 ./usr/bin/racon
-rwxr-xr-x root/root 9854 2021-09-01 15:17 ./usr/bin/racon_wrapper.py
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/lib/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/lib/racon/
-rwxr-xr-x root/root 550540 2021-09-01 15:17 ./usr/lib/racon/racon_test
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/share/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/share/doc/racon/
-rw-r--r-- root/root 953 2021-09-01 15:17 ./usr/share/doc/racon/changelog.Debian.gz
-rw-r--r-- root/root 1481 2021-09-01 15:17 ./usr/share/doc/racon/copyright
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/share/doc/racon/examples/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/share/doc/racon/examples/data/
-rw-r--r-- root/root 146882 2021-09-01 15:17 ./usr/share/doc/racon/examples/data/sample_ava_overlaps.mhap.gz
-rw-r--r-- root/root 151632 2021-09-01 15:17 ./usr/share/doc/racon/examples/data/sample_ava_overlaps.paf.gz
-rw-r--r-- root/root 14197 2021-09-01 15:17 ./usr/share/doc/racon/examples/data/sample_layout.fasta.gz
-rw-r--r-- root/root 5111 2021-09-01 15:17 ./usr/share/doc/racon/examples/data/sample_overlaps.paf.gz
-rw-r--r-- root/root 698977 2021-09-01 15:17 ./usr/share/doc/racon/examples/data/sample_overlaps.sam.gz
-rw-r--r-- root/root 488701 2021-09-01 15:17 ./usr/share/doc/racon/examples/data/sample_reads.fasta.gz
-rw-r--r-- root/root 1526281 2021-09-01 15:17 ./usr/share/doc/racon/examples/data/sample_reads.fastq.gz
-rw-r--r-- root/root 15195 2021-09-01 15:17 ./usr/share/doc/racon/examples/data/sample_reference.fasta.gz
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/share/lintian/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 114 2021-09-01 15:17 ./usr/share/lintian/overrides/racon
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/share/man/
drwxr-xr-x root/root 0 2021-09-01 15:17 ./usr/share/man/man1/
-rw-r--r-- root/root 1472 2021-09-01 15:17 ./usr/share/man/man1/racon.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 44840
Build-Time: 2296
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 298
Job: racon_1.4.21-1
Machine Architecture: armhf
Package: racon
Package-Time: 2619
Source-Version: 1.4.21-1
Space: 44840
Status: successful
Version: 1.4.21-1
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Finished at 2021-09-04T08:10:19Z
Build needed 00:43:39, 44840k disk space