racon →
1.5.0-2 →
armhf → 2022-01-02 07:11:36
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| racon 1.5.0-2 (armhf) Sun, 02 Jan 2022 06:47:34 +0000 |
+==============================================================================+
Package: racon
Version: 1.5.0-2
Source Version: 1.5.0-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-ea9a8733-0d4b-44b7-bda8-e9412a8a6a06' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [12.7 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.6 MB]
Fetched 26.2 MB in 10s (2572 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 3107 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main racon 1.5.0-2 (dsc) [2106 B]
Get:2 http://172.17.4.1/private bookworm-staging/main racon 1.5.0-2 (tar) [3084 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main racon 1.5.0-2 (diff) [20.6 kB]
Fetched 3107 kB in 1s (4300 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/racon-3ub3sk/racon-1.5.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/racon-3ub3sk' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-ZlvexN/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-ZlvexN/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-ZlvexN/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (10.3 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 47 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (68.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12559 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), cmake, libgtest-dev, libbioparser-dev, libcereal-dev, libedlib-dev (>= 1.2.7-3~), libspoa-dev, libthread-pool-dev (>= 3.0.2), rampler
Filtered Build-Depends: debhelper-compat (= 13), cmake, libgtest-dev, libbioparser-dev, libcereal-dev, libedlib-dev (>= 1.2.7-3~), libspoa-dev, libthread-pool-dev (>= 3.0.2), rampler
dpkg-deb: building package 'sbuild-build-depends-racon-dummy' in '/<<BUILDDIR>>/resolver-ZlvexN/apt_archive/sbuild-build-depends-racon-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-racon-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ Sources [558 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ Packages [643 B]
Fetched 2534 B in 0s (12.3 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install racon build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file gettext gettext-base googletest groff-base
intltool-debian libarchive-zip-perl libarchive13 libbioparser-dev
libbiosoup-dev libbrotli1 libcereal-dev libcurl4 libdebhelper-perl
libedlib-dev libedlib1 libelf1 libexpat1 libfile-stripnondeterminism-perl
libgtest-dev libicu67 libjsoncpp25 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 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 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-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file gettext gettext-base googletest groff-base
intltool-debian libarchive-zip-perl libarchive13 libbioparser-dev
libbiosoup-dev libbrotli1 libcereal-dev libcurl4 libdebhelper-perl
libedlib-dev libedlib1 libelf1 libexpat1 libfile-stripnondeterminism-perl
libgtest-dev libicu67 libjsoncpp25 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-racon-dummy zlib1g-dev
0 upgraded, 62 newly installed, 0 to remove and 47 not upgraded.
Need to get 27.7 MB of archives.
After this operation, 117 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ZlvexN/apt_archive ./ sbuild-build-depends-racon-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-5 [136 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-2 [31.5 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.9.4-4 [1308 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3-1 [79.8 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-5 [60.5 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-5 [475 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libarchive13 armhf 3.5.2-1 [301 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.80.0-3 [322 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.2-1 [80.1 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp25 armhf 1.9.5-2 [67.0 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf librhash0 armhf 1.4.2-1 [141 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libuv1 armhf 1.42.0-1 [121 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf dh-elpa-helper all 2.0.10 [11.3 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf emacsen-common all 3.0.4 [19.3 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf cmake-data all 3.22.1-1 [1905 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf cmake armhf 3.22.1-1+b1 [3478 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf googletest all 1.11.0-3 [535 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libbiosoup-dev all 0.10.0-4 [7784 B]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libbioparser-dev all 3.0.15-2 [9028 B]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf rapidjson-dev all 1.1.0+dfsg2-7 [98.9 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libcereal-dev all 1.3.0+dfsg-2 [210 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libedlib1 armhf 1.2.7-3 [14.1 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libedlib-dev armhf 1.2.7-3 [18.9 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libgtest-dev armhf 1.11.0-3 [1397 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libspoa7.0.0 armhf 4.0.7+ds-2 [51.4 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libspoa-dev armhf 4.0.7+ds-2 [6772 B]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libthread-pool-dev all 3.0.2-1 [4376 B]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf rampler armhf 2.0.0-2 [19.2 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-5) ...
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Setting up libbiosoup-dev (0.10.0-4) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libuv1:armhf (1.42.0-1) ...
Setting up emacsen-common (3.0.4) ...
Setting up rampler (2.0.0-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up dh-elpa-helper (2.0.10) ...
Setting up libncurses6:armhf (6.3-1) ...
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-2) ...
Setting up autopoint (0.21-4) ...
Setting up libjsoncpp25:armhf (1.9.5-2) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libedlib1:armhf (1.2.7-3) ...
Setting up libbioparser-dev (3.0.15-2) ...
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 (1.10.0-2) ...
Setting up cmake-data (3.22.1-1) ...
Setting up libelf1:armhf (0.186-1) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libprocps8:armhf (2:3.3.17-5) ...
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up gettext (0.21-4) ...
Setting up libgtest-dev:armhf (1.11.0-3) ...
Setting up libtool (2.4.6-15) ...
Setting up libarchive13:armhf (3.5.2-1) ...
Setting up libcereal-dev (1.3.0+dfsg-2) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libedlib-dev:armhf (1.2.7-3) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-8) ...
Setting up procps (2:3.3.17-5) ...
Setting up libcurl4:armhf (7.80.0-3) ...
Setting up automake (1:1.16.5-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libspoa-dev:armhf (4.0.7+ds-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-4) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up cmake (3.22.1-1+b1) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-racon-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-163-generic armhf (armv8l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-11_11.2.0-10+rpi1 gcc-11_11.2.0-10+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.16-1+rpi1
Package versions: adduser_3.118 apt_2.3.12 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3.1 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-5 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 cmake_3.22.1-1+b1 cmake-data_3.22.1-1 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-elpa-helper_2.0.10 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 emacsen-common_3.0.4 fakeroot_1.25.3-1.1 file_1:5.41-2 findutils_4.8.0-1 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-10+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-10+rpi1 gcc-11-base_11.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 googletest_1.11.0-3 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_3.7-1 groff-base_1.22.4-8 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.12 libarchive-zip-perl_1.68-1 libarchive13_3.5.2-1 libasan6_11.2.0-10+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-10+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-5+rpi1 libbioparser-dev_3.0.15-2 libbiosoup-dev_0.10.0-4 libblkid1_2.37.2-4 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10+rpi1 libcereal-dev_1.3.0+dfsg-2 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.26-1 libcrypt1_1:4.4.26-1 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl4_7.80.0-3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libedlib-dev_1.2.7-3 libedlib1_1.2.7-3 libelf1_0.186-1 libexpat1_2.4.2-1 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.2.0-10+rpi1 libgcc-s1_11.2.0-10+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.2-2 libgomp1_11.2.0-10+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libgtest-dev_1.11.0-3 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libjsoncpp25_1.9.5-2 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libncurses6_6.3-1 libncursesw6_6.3-1 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.4-2 libprocps8_2:3.3.17-5 libpsl5_0.21.0-1.2 libreadline8_8.1-2 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg2-2 libsasl2-modules-db_2.1.27+dfsg2-2 libseccomp2_2.5.3-2+rpi1 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libspoa-dev_4.0.7+ds-2 libspoa7.0.0_4.0.7+ds-2 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl1.1_1.1.1l-1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.7-1+rpi1 libtasn1-6_4.18.0-4 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libthread-pool-dev_3.0.2-1 libtinfo6_6.3-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_249.7-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libuv1_1.42.0-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.16-1+rpi1 login_1:4.8.1-2 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-4 mawk_1.3.4.20200120-2 mount_2.37.2-4 ncurses-base_6.3-1 ncurses-bin_6.3-1 netbase_6.3 passwd_1:4.8.1-2 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 procps_2:3.3.17-5 rampler_2.0.0-2 rapidjson-dev_1.1.0+dfsg2-7 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-racon-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.MaEIuzRT/trustedkeys.kbx': General error
gpgv: Signature made Fri Dec 31 11:44:31 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./racon_1.5.0-2.dsc
dpkg-source: info: extracting racon in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking racon_1.5.0.orig.tar.gz
dpkg-source: info: unpacking racon_1.5.0-2.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
dpkg-source: info: applying make-compatible-with-old-threadpool.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-ea9a8733-0d4b-44b7-bda8-e9412a8a6a06
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package racon
dpkg-buildpackage: info: source version 1.5.0-2
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 CXX compiler identification is GNU 11.2.0
-- 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
-- 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
-- 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'
/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[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f CMakeFiles/racon.dir/build.make CMakeFiles/racon.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/racon.dir/DependInfo.cmake --color=
make[3]: Leaving 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
/<<PKGBUILDDIR>>/src/overlap.cpp:219:54: warning: format '%zu' expects argument of type 'size_t', but argument 4 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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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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cd test && ../obj-*/bin/racon_test
Running main() from ./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 (1 ms)
[ RUN ] RaconInitializeTest.WindowLengthError
[ OK ] RaconInitializeTest.WindowLengthError (1 ms)
[ RUN ] RaconInitializeTest.SequencesPathExtensionError
[ OK ] RaconInitializeTest.SequencesPathExtensionError (1 ms)
[ RUN ] RaconInitializeTest.OverlapsPathExtensionError
[ OK ] RaconInitializeTest.OverlapsPathExtensionError (5 ms)
[ RUN ] RaconInitializeTest.TargetPathExtensionError
[ OK ] RaconInitializeTest.TargetPathExtensionError (5 ms)
[----------] 5 tests from RaconInitializeTest (15 ms total)
[----------] 10 tests from RaconPolishingTest
[ RUN ] RaconPolishingTest.ConsensusWithQualities
[racon::Polisher::initialize] loaded target sequences 0.001118 s
[racon::Polisher::initialize] loaded sequences 0.087650 s
[racon::Polisher::initialize] loaded overlaps 0.001321 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.051542 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.081242 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.100047 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.133976 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.156921 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.176627 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.214523 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.247068 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.272751 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.307190 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.331320 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.363239 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.406161 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.429997 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.466696 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.502736 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.527906 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.558819 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.593325 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.640484 s
[racon::Polisher::initialize] transformed data into windows 0.011175 s
[racon::Polisher::polish] generating consensus [=> ] 0.516693 s
[racon::Polisher::polish] generating consensus [==> ] 0.990612 s
[racon::Polisher::polish] generating consensus [===> ] 1.427535 s
[racon::Polisher::polish] generating consensus [====> ] 1.730148 s
[racon::Polisher::polish] generating consensus [=====> ] 1.945946 s
[racon::Polisher::polish] generating consensus [======> ] 2.128286 s
[racon::Polisher::polish] generating consensus [=======> ] 2.335126 s
[racon::Polisher::polish] generating consensus [========> ] 2.629268 s
[racon::Polisher::polish] generating consensus [=========> ] 2.942087 s
[racon::Polisher::polish] generating consensus [==========> ] 3.359133 s
[racon::Polisher::polish] generating consensus [===========> ] 3.954167 s
[racon::Polisher::polish] generating consensus [============> ] 4.596227 s
[racon::Polisher::polish] generating consensus [=============> ] 5.513011 s
[racon::Polisher::polish] generating consensus [==============> ] 6.425711 s
[racon::Polisher::polish] generating consensus [===============> ] 7.041545 s
[racon::Polisher::polish] generating consensus [================> ] 7.597664 s
[racon::Polisher::polish] generating consensus [=================> ] 8.153946 s
[racon::Polisher::polish] generating consensus [==================> ] 8.603401 s
[racon::Polisher::polish] generating consensus [===================>] 9.129920 s
[racon::Polisher::polish] generating consensus [====================] 11.488547 s
[racon::Polisher::] total = 12.264990 s
[ OK ] RaconPolishingTest.ConsensusWithQualities (12274 ms)
[ RUN ] RaconPolishingTest.ConsensusWithoutQualities
[racon::Polisher::initialize] loaded target sequences 0.000992 s
[racon::Polisher::initialize] loaded sequences 0.032604 s
[racon::Polisher::initialize] loaded overlaps 0.001212 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.049573 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.079925 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.098727 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.132814 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.155725 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.175481 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.213089 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.244042 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.270942 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.305671 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.329841 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.361821 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.402765 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.426716 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.463926 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.500026 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.526455 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.557548 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.591076 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.638115 s
[racon::Polisher::initialize] transformed data into windows 0.004471 s
[racon::Polisher::polish] generating consensus [=> ] 0.566461 s
[racon::Polisher::polish] generating consensus [==> ] 1.201173 s
[racon::Polisher::polish] generating consensus [===> ] 1.704886 s
[racon::Polisher::polish] generating consensus [====> ] 2.099042 s
[racon::Polisher::polish] generating consensus [=====> ] 2.386299 s
[racon::Polisher::polish] generating consensus [======> ] 2.651725 s
[racon::Polisher::polish] generating consensus [=======> ] 2.959544 s
[racon::Polisher::polish] generating consensus [========> ] 3.370890 s
[racon::Polisher::polish] generating consensus [=========> ] 3.825553 s
[racon::Polisher::polish] generating consensus [==========> ] 4.509640 s
[racon::Polisher::polish] generating consensus [===========> ] 5.241711 s
[racon::Polisher::polish] generating consensus [============> ] 6.123771 s
[racon::Polisher::polish] generating consensus [=============> ] 7.390292 s
[racon::Polisher::polish] generating consensus [==============> ] 8.302855 s
[racon::Polisher::polish] generating consensus [===============> ] 9.255633 s
[racon::Polisher::polish] generating consensus [================> ] 9.997558 s
[racon::Polisher::polish] generating consensus [=================> ] 10.842646 s
[racon::Polisher::polish] generating consensus [==================> ] 11.293094 s
[racon::Polisher::polish] generating consensus [===================>] 11.966065 s
[racon::Polisher::polish] generating consensus [====================] 15.547588 s
[racon::Polisher::] total = 16.257420 s
[ OK ] RaconPolishingTest.ConsensusWithoutQualities (16266 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments
[racon::Polisher::initialize] loaded target sequences 0.000995 s
[racon::Polisher::initialize] loaded sequences 0.085070 s
[racon::Polisher::initialize] loaded overlaps 0.040479 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.017349 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.017435 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.017506 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.017578 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.017646 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.017719 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.017790 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.017860 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.017930 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.018010 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.018080 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.018151 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.018218 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.018284 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.018350 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.018416 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.018482 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.018548 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.018615 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.018682 s
[racon::Polisher::initialize] transformed data into windows 0.010381 s
[racon::Polisher::polish] generating consensus [=> ] 0.539179 s
[racon::Polisher::polish] generating consensus [==> ] 1.021875 s
[racon::Polisher::polish] generating consensus [===> ] 1.479158 s
[racon::Polisher::polish] generating consensus [====> ] 1.783080 s
[racon::Polisher::polish] generating consensus [=====> ] 1.985166 s
[racon::Polisher::polish] generating consensus [======> ] 2.163021 s
[racon::Polisher::polish] generating consensus [=======> ] 2.384805 s
[racon::Polisher::polish] generating consensus [========> ] 2.675071 s
[racon::Polisher::polish] generating consensus [=========> ] 2.909600 s
[racon::Polisher::polish] generating consensus [==========> ] 3.337969 s
[racon::Polisher::polish] generating consensus [===========> ] 3.923806 s
[racon::Polisher::polish] generating consensus [============> ] 4.590554 s
[racon::Polisher::polish] generating consensus [=============> ] 5.549088 s
[racon::Polisher::polish] generating consensus [==============> ] 6.411647 s
[racon::Polisher::polish] generating consensus [===============> ] 7.082368 s
[racon::Polisher::polish] generating consensus [================> ] 7.593223 s
[racon::Polisher::polish] generating consensus [=================> ] 8.277934 s
[racon::Polisher::polish] generating consensus [==================> ] 8.676744 s
[racon::Polisher::polish] generating consensus [===================>] 9.144697 s
[racon::Polisher::polish] generating consensus [====================] 11.280589 s
[racon::Polisher::] total = 11.470643 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments (11479 ms)
[ RUN ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments
[racon::Polisher::initialize] loaded target sequences 0.000990 s
[racon::Polisher::initialize] loaded sequences 0.032505 s
[racon::Polisher::initialize] loaded overlaps 0.040605 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.017069 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.017154 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.017223 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.017294 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.017363 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.017432 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.017503 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.017574 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.017644 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.017715 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.017783 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.017853 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.017919 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.017984 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.018050 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.018117 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.018182 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.018247 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.018313 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.018378 s
[racon::Polisher::initialize] transformed data into windows 0.004135 s
[racon::Polisher::polish] generating consensus [=> ] 0.538313 s
[racon::Polisher::polish] generating consensus [==> ] 1.108166 s
[racon::Polisher::polish] generating consensus [===> ] 1.597262 s
[racon::Polisher::polish] generating consensus [====> ] 1.993989 s
[racon::Polisher::polish] generating consensus [=====> ] 2.234711 s
[racon::Polisher::polish] generating consensus [======> ] 2.505817 s
[racon::Polisher::polish] generating consensus [=======> ] 2.774499 s
[racon::Polisher::polish] generating consensus [========> ] 3.197395 s
[racon::Polisher::polish] generating consensus [=========> ] 3.562000 s
[racon::Polisher::polish] generating consensus [==========> ] 4.216610 s
[racon::Polisher::polish] generating consensus [===========> ] 4.886400 s
[racon::Polisher::polish] generating consensus [============> ] 5.709566 s
[racon::Polisher::polish] generating consensus [=============> ] 6.970839 s
[racon::Polisher::polish] generating consensus [==============> ] 7.923292 s
[racon::Polisher::polish] generating consensus [===============> ] 8.769642 s
[racon::Polisher::polish] generating consensus [================> ] 9.570563 s
[racon::Polisher::polish] generating consensus [=================> ] 10.383366 s
[racon::Polisher::polish] generating consensus [==================> ] 10.799841 s
[racon::Polisher::polish] generating consensus [===================>] 11.301550 s
[racon::Polisher::polish] generating consensus [====================] 14.341778 s
[racon::Polisher::] total = 14.463653 s
[ OK ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments (14473 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow
[racon::Polisher::initialize] loaded target sequences 0.000997 s
[racon::Polisher::initialize] loaded sequences 0.085142 s
[racon::Polisher::initialize] loaded overlaps 0.001206 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.049610 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.080140 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.099425 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.133685 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.157134 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.175911 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.213998 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.248148 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.272768 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.308905 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.333252 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.364792 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.408360 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.431281 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.468488 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.504609 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.530242 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.564004 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.595847 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.643038 s
[racon::Polisher::initialize] transformed data into windows 0.009272 s
[racon::Polisher::polish] generating consensus [=> ] 1.859382 s
[racon::Polisher::polish] generating consensus [==> ] 1.859526 s
[racon::Polisher::polish] generating consensus [===> ] 3.462420 s
[racon::Polisher::polish] generating consensus [====> ] 3.463513 s
[racon::Polisher::polish] generating consensus [=====> ] 3.901907 s
[racon::Polisher::polish] generating consensus [======> ] 4.250268 s
[racon::Polisher::polish] generating consensus [=======> ] 4.601723 s
[racon::Polisher::polish] generating consensus [========> ] 5.239687 s
[racon::Polisher::polish] generating consensus [=========> ] 5.771226 s
[racon::Polisher::polish] generating consensus [==========> ] 6.865346 s
[racon::Polisher::polish] generating consensus [===========> ] 7.906378 s
[racon::Polisher::polish] generating consensus [============> ] 9.232091 s
[racon::Polisher::polish] generating consensus [=============> ] 10.981145 s
[racon::Polisher::polish] generating consensus [==============> ] 12.312994 s
[racon::Polisher::polish] generating consensus [===============> ] 13.563870 s
[racon::Polisher::polish] generating consensus [================> ] 14.403122 s
[racon::Polisher::polish] generating consensus [=================> ] 15.710863 s
[racon::Polisher::polish] generating consensus [==================> ] 15.992201 s
[racon::Polisher::polish] generating consensus [===================>] 17.470298 s
[racon::Polisher::polish] generating consensus [====================] 21.452883 s
[racon::Polisher::] total = 22.231430 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow (22248 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesEditDistance
[racon::Polisher::initialize] loaded target sequences 0.000994 s
[racon::Polisher::initialize] loaded sequences 0.086348 s
[racon::Polisher::initialize] loaded overlaps 0.001266 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.049387 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.079953 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.098844 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.132907 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.156173 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.176049 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.215145 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.247440 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.273608 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.307715 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.332531 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.365546 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.407587 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.431656 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.469102 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.505758 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.531429 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.564752 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.598057 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.645866 s
[racon::Polisher::initialize] transformed data into windows 0.011545 s
[racon::Polisher::polish] generating consensus [=> ] 0.498417 s
[racon::Polisher::polish] generating consensus [==> ] 0.959951 s
[racon::Polisher::polish] generating consensus [===> ] 1.386593 s
[racon::Polisher::polish] generating consensus [====> ] 1.676138 s
[racon::Polisher::polish] generating consensus [=====> ] 1.884653 s
[racon::Polisher::polish] generating consensus [======> ] 2.060040 s
[racon::Polisher::polish] generating consensus [=======> ] 2.261027 s
[racon::Polisher::polish] generating consensus [========> ] 2.544267 s
[racon::Polisher::polish] generating consensus [=========> ] 2.842289 s
[racon::Polisher::polish] generating consensus [==========> ] 3.246649 s
[racon::Polisher::polish] generating consensus [===========> ] 3.813161 s
[racon::Polisher::polish] generating consensus [============> ] 4.435984 s
[racon::Polisher::polish] generating consensus [=============> ] 5.271389 s
[racon::Polisher::polish] generating consensus [==============> ] 6.192378 s
[racon::Polisher::polish] generating consensus [===============> ] 6.787739 s
[racon::Polisher::polish] generating consensus [================> ] 7.327112 s
[racon::Polisher::polish] generating consensus [=================> ] 7.855001 s
[racon::Polisher::polish] generating consensus [==================> ] 8.271674 s
[racon::Polisher::polish] generating consensus [===================>] 8.771611 s
[racon::Polisher::polish] generating consensus [====================] 11.021827 s
[racon::Polisher::] total = 11.801396 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesEditDistance (11810 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualities
[racon::Polisher::initialize] loaded target sequences 0.085053 s
[racon::Polisher::initialize] loaded sequences 0.087898 s
[racon::Polisher::initialize] loaded overlaps 0.043259 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.050927 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.082908 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.115906 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.138509 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.166760 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.184928 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.215856 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.231320 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.262511 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.305573 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.327013 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.366394 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.408583 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.446344 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.486022 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.526063 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.555885 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.608756 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.636692 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.730219 s
[racon::Polisher::initialize] transformed data into windows 0.045001 s
[racon::Polisher::polish] generating consensus [=> ] 0.429423 s
[racon::Polisher::polish] generating consensus [==> ] 0.842088 s
[racon::Polisher::polish] generating consensus [===> ] 1.245343 s
[racon::Polisher::polish] generating consensus [====> ] 1.248725 s
[racon::Polisher::polish] generating consensus [=====> ] 1.572710 s
[racon::Polisher::polish] generating consensus [======> ] 1.760488 s
[racon::Polisher::polish] generating consensus [=======> ] 2.060781 s
[racon::Polisher::polish] generating consensus [========> ] 2.078945 s
[racon::Polisher::polish] generating consensus [=========> ] 2.629496 s
[racon::Polisher::polish] generating consensus [==========> ] 2.859436 s
[racon::Polisher::polish] generating consensus [===========> ] 3.066619 s
[racon::Polisher::polish] generating consensus [============> ] 3.144319 s
[racon::Polisher::polish] generating consensus [=============> ] 3.411914 s
[racon::Polisher::polish] generating consensus [==============> ] 3.415549 s
[racon::Polisher::polish] generating consensus [===============> ] 3.988881 s
[racon::Polisher::polish] generating consensus [================> ] 3.991998 s
[racon::Polisher::polish] generating consensus [=================> ] 5.019352 s
[racon::Polisher::polish] generating consensus [==================> ] 5.414568 s
[racon::Polisher::polish] generating consensus [===================>] 5.843229 s
[racon::Polisher::polish] generating consensus [====================] 6.077061 s
[racon::Polisher::] total = 7.073699 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualities (7081 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull
[racon::Polisher::initialize] loaded target sequences 0.084998 s
[racon::Polisher::initialize] loaded sequences 0.087192 s
[racon::Polisher::initialize] loaded overlaps 0.032187 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.786654 s
[racon::Polisher::initialize] aligning overlaps [==> ] 1.337431 s
[racon::Polisher::initialize] aligning overlaps [===> ] 1.840352 s
[racon::Polisher::initialize] aligning overlaps [====> ] 2.542417 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 3.092311 s
[racon::Polisher::initialize] aligning overlaps [======> ] 3.570199 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 4.187948 s
[racon::Polisher::initialize] aligning overlaps [========> ] 4.947755 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 5.719872 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 6.412760 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 6.978151 s
[racon::Polisher::initialize] aligning overlaps [============> ] 7.775032 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 8.599409 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 9.303969 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 10.137901 s
[racon::Polisher::initialize] aligning overlaps [================> ] 10.948003 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 11.690677 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 12.490122 s
[racon::Polisher::initialize] aligning overlaps [===================>] 13.320978 s
[racon::Polisher::initialize] aligning overlaps [====================] 14.098664 s
[racon::Polisher::initialize] transformed data into windows 0.328244 s
[racon::Polisher::polish] generating consensus [=> ] 18.771020 s
[racon::Polisher::polish] generating consensus [==> ] 31.951746 s
[racon::Polisher::polish] generating consensus [===> ] 47.154726 s
[racon::Polisher::polish] generating consensus [====> ] 59.324705 s
[racon::Polisher::polish] generating consensus [=====> ] 73.484020 s
[racon::Polisher::polish] generating consensus [======> ] 89.871799 s
[racon::Polisher::polish] generating consensus [=======> ] 105.858154 s
[racon::Polisher::polish] generating consensus [========> ] 117.702097 s
[racon::Polisher::polish] generating consensus [=========> ] 132.409892 s
[racon::Polisher::polish] generating consensus [==========> ] 150.238015 s
[racon::Polisher::polish] generating consensus [===========> ] 165.275052 s
[racon::Polisher::polish] generating consensus [============> ] 182.215236 s
[racon::Polisher::polish] generating consensus [=============> ] 196.552306 s
[racon::Polisher::polish] generating consensus [==============> ] 212.584183 s
[racon::Polisher::polish] generating consensus [===============> ] 229.032479 s
[racon::Polisher::polish] generating consensus [================> ] 238.534920 s
[racon::Polisher::polish] generating consensus [=================> ] 256.484082 s
[racon::Polisher::polish] generating consensus [==================> ] 273.244270 s
[racon::Polisher::polish] generating consensus [===================>] 289.624667 s
[racon::Polisher::polish] generating consensus [====================] 305.203779 s
[racon::Polisher::] total = 319.889802 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull (319899 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull
[racon::Polisher::initialize] loaded target sequences 0.032478 s
[racon::Polisher::initialize] loaded sequences 0.033260 s
[racon::Polisher::initialize] loaded overlaps 0.031920 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.781784 s
[racon::Polisher::initialize] aligning overlaps [==> ] 1.323756 s
[racon::Polisher::initialize] aligning overlaps [===> ] 1.815700 s
[racon::Polisher::initialize] aligning overlaps [====> ] 2.504449 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 3.044014 s
[racon::Polisher::initialize] aligning overlaps [======> ] 3.508227 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 4.104467 s
[racon::Polisher::initialize] aligning overlaps [========> ] 4.848490 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 5.606037 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 6.282347 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 6.833988 s
[racon::Polisher::initialize] aligning overlaps [============> ] 7.614015 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 8.423797 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 9.123778 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 9.956589 s
[racon::Polisher::initialize] aligning overlaps [================> ] 10.767825 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 11.511307 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 12.309956 s
[racon::Polisher::initialize] aligning overlaps [===================>] 13.140041 s
[racon::Polisher::initialize] aligning overlaps [====================] 13.917523 s
[racon::Polisher::initialize] transformed data into windows 0.159743 s
[racon::Polisher::polish] generating consensus [=> ] 25.879901 s
[racon::Polisher::polish] generating consensus [==> ] 44.797134 s
[racon::Polisher::polish] generating consensus [===> ] 65.609018 s
[racon::Polisher::polish] generating consensus [====> ] 81.170672 s
[racon::Polisher::polish] generating consensus [=====> ] 100.592828 s
[racon::Polisher::polish] generating consensus [======> ] 121.959376 s
[racon::Polisher::polish] generating consensus [=======> ] 144.066918 s
[racon::Polisher::polish] generating consensus [========> ] 160.672769 s
[racon::Polisher::polish] generating consensus [=========> ] 180.904593 s
[racon::Polisher::polish] generating consensus [==========> ] 205.586554 s
[racon::Polisher::polish] generating consensus [===========> ] 226.562082 s
[racon::Polisher::polish] generating consensus [============> ] 249.054901 s
[racon::Polisher::polish] generating consensus [=============> ] 269.657595 s
[racon::Polisher::polish] generating consensus [==============> ] 291.578785 s
[racon::Polisher::polish] generating consensus [===============> ] 312.752482 s
[racon::Polisher::polish] generating consensus [================> ] 324.400783 s
[racon::Polisher::polish] generating consensus [=================> ] 350.984837 s
[racon::Polisher::polish] generating consensus [==================> ] 375.801797 s
[racon::Polisher::polish] generating consensus [===================>] 398.745522 s
[racon::Polisher::polish] generating consensus [====================] 419.983288 s
[racon::Polisher::] total = 434.211462 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull (434221 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap
[racon::Polisher::initialize] loaded target sequences 0.085298 s
[racon::Polisher::initialize] loaded sequences 0.086223 s
[racon::Polisher::initialize] loaded overlaps 0.032355 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.783446 s
[racon::Polisher::initialize] aligning overlaps [==> ] 1.326689 s
[racon::Polisher::initialize] aligning overlaps [===> ] 1.819101 s
[racon::Polisher::initialize] aligning overlaps [====> ] 2.507498 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 3.048742 s
[racon::Polisher::initialize] aligning overlaps [======> ] 3.516452 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 4.116222 s
[racon::Polisher::initialize] aligning overlaps [========> ] 4.866627 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 5.625193 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 6.304567 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 6.858486 s
[racon::Polisher::initialize] aligning overlaps [============> ] 7.639620 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 8.450260 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 9.148564 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 9.980691 s
[racon::Polisher::initialize] aligning overlaps [================> ] 10.790609 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 11.534041 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 12.333213 s
[racon::Polisher::initialize] aligning overlaps [===================>] 13.163520 s
[racon::Polisher::initialize] aligning overlaps [====================] 13.941414 s
[racon::Polisher::initialize] transformed data into windows 0.330939 s
[racon::Polisher::polish] generating consensus [=> ] 18.782404 s
[racon::Polisher::polish] generating consensus [==> ] 31.956126 s
[racon::Polisher::polish] generating consensus [===> ] 47.128129 s
[racon::Polisher::polish] generating consensus [====> ] 59.289354 s
[racon::Polisher::polish] generating consensus [=====> ] 73.431812 s
[racon::Polisher::polish] generating consensus [======> ] 89.690084 s
[racon::Polisher::polish] generating consensus [=======> ] 105.693607 s
[racon::Polisher::polish] generating consensus [========> ] 117.520490 s
[racon::Polisher::polish] generating consensus [=========> ] 132.215555 s
[racon::Polisher::polish] generating consensus [==========> ] 150.021325 s
[racon::Polisher::polish] generating consensus [===========> ] 165.048437 s
[racon::Polisher::polish] generating consensus [============> ] 181.978518 s
[racon::Polisher::polish] generating consensus [=============> ] 196.276232 s
[racon::Polisher::polish] generating consensus [==============> ] 212.313965 s
[racon::Polisher::polish] generating consensus [===============> ] 228.740503 s
[racon::Polisher::polish] generating consensus [================> ] 238.233346 s
[racon::Polisher::polish] generating consensus [=================> ] 256.164241 s
[racon::Polisher::polish] generating consensus [==================> ] 272.925637 s
[racon::Polisher::polish] generating consensus [===================>] 289.265433 s
[racon::Polisher::polish] generating consensus [====================] 304.843561 s
[racon::Polisher::] total = 319.373832 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap (319383 ms)
[----------] 10 tests from RaconPolishingTest (1169139 ms total)
[----------] Global test environment tear-down
[==========] 15 tests from 2 test suites ran. (1169155 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 -O--buildsystem=cmake
dh_strip -a -O--buildsystem=cmake
dh_makeshlibs -a -O--buildsystem=cmake
dh_shlibdeps -a -O--buildsystem=cmake
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/bin/racon was not linked against ld-linux-armhf.so.3 (it uses 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-dbgsym' in '../racon-dbgsym_1.5.0-2_armhf.deb'.
dpkg-deb: building package 'racon' in '../racon_1.5.0-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../racon_1.5.0-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-01-02T07:11:33Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
racon_1.5.0-2_armhf.changes:
----------------------------
Format: 1.8
Date: Fri, 31 Dec 2021 17:08:40 +0530
Source: racon
Binary: racon racon-dbgsym
Architecture: armhf
Version: 1.5.0-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
racon - consensus module for raw de novo DNA assembly of long uncorrected
Changes:
racon (1.5.0-2) unstable; urgency=medium
.
* Team Upload.
[ Andreas Tille ]
* Add run-unit-test as user example
* DEP3
.
[ Nilesh Patra ]
* Revert md5sum based change in autopkgtest
* Versioned B-D on edlib
Checksums-Sha1:
2ce186def3dbf3d2f99b8fac09566ffd8f9a693f 1112676 racon-dbgsym_1.5.0-2_armhf.deb
8c48d3c69aa3f52d1a3833544d3a467b11497e8d 5986 racon_1.5.0-2_armhf.buildinfo
156f3d296d738fa76fdf0ea519194ebb7fd7c657 3102824 racon_1.5.0-2_armhf.deb
Checksums-Sha256:
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Files:
9d8a4daa113343a30afa4e544cf5c16e 1112676 debug optional racon-dbgsym_1.5.0-2_armhf.deb
136436fe7975e8acb4868a971ef32287 5986 science optional racon_1.5.0-2_armhf.buildinfo
67f4f3b5a141f7a29c74e0f2307567fb 3102824 science optional racon_1.5.0-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
racon-dbgsym_1.5.0-2_armhf.deb
------------------------------
new Debian package, version 2.0.
size 1112676 bytes: control archive=532 bytes.
363 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: racon-dbgsym
Source: racon
Version: 1.5.0-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1161
Depends: racon (= 1.5.0-2)
Section: debug
Priority: optional
Description: debug symbols for racon
Build-Ids: 08b62f01fea95d8c14088c3cf77296dbeb52f04e
drwxr-xr-x root/root 0 2021-12-31 11:38 ./
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/lib/
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/lib/debug/.build-id/08/
-rw-r--r-- root/root 1177960 2021-12-31 11:38 ./usr/lib/debug/.build-id/08/b62f01fea95d8c14088c3cf77296dbeb52f04e.debug
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/share/
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-12-31 11:38 ./usr/share/doc/racon-dbgsym -> racon
racon_1.5.0-2_armhf.deb
-----------------------
new Debian package, version 2.0.
size 3102824 bytes: control archive=1856 bytes.
2118 bytes, 41 lines control
1249 bytes, 16 lines md5sums
Package: racon
Version: 1.5.0-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3134
Depends: libc6 (>= 2.4), libedlib1 (>= 1.2.7-3~), libgcc-s1 (>= 3.5), libspoa7.0.0 (>= 4.0.7+ds), libstdc++6 (>= 11), 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 2021-12-31 11:38 ./
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/bin/
-rwxr-xr-x root/root 124632 2021-12-31 11:38 ./usr/bin/racon
-rwxr-xr-x root/root 10415 2021-12-31 11:38 ./usr/bin/racon_wrapper.py
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/share/
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/share/doc/racon/
-rw-r--r-- root/root 278 2021-12-31 11:36 ./usr/share/doc/racon/README.test
-rw-r--r-- root/root 1199 2021-12-31 11:38 ./usr/share/doc/racon/changelog.Debian.gz
-rw-r--r-- root/root 1647 2021-12-31 11:31 ./usr/share/doc/racon/copyright
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/share/doc/racon/examples/
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/share/doc/racon/examples/data/
-rw-r--r-- root/root 146882 2021-12-31 11:38 ./usr/share/doc/racon/examples/data/sample_ava_overlaps.mhap.gz
-rw-r--r-- root/root 151632 2021-12-31 11:38 ./usr/share/doc/racon/examples/data/sample_ava_overlaps.paf.gz
-rw-r--r-- root/root 14197 2021-12-31 11:38 ./usr/share/doc/racon/examples/data/sample_layout.fasta.gz
-rw-r--r-- root/root 5111 2021-12-31 11:38 ./usr/share/doc/racon/examples/data/sample_overlaps.paf.gz
-rw-r--r-- root/root 698977 2021-12-31 11:38 ./usr/share/doc/racon/examples/data/sample_overlaps.sam.gz
-rw-r--r-- root/root 488701 2021-12-31 11:38 ./usr/share/doc/racon/examples/data/sample_reads.fasta.gz
-rw-r--r-- root/root 1526281 2021-12-31 11:38 ./usr/share/doc/racon/examples/data/sample_reads.fastq.gz
-rw-r--r-- root/root 15195 2021-12-31 11:38 ./usr/share/doc/racon/examples/data/sample_reference.fasta.gz
-rw-r--r-- root/root 566 2021-12-31 11:35 ./usr/share/doc/racon/run-unit-test
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/share/lintian/
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 114 2021-12-19 16:38 ./usr/share/lintian/overrides/racon
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/share/man/
drwxr-xr-x root/root 0 2021-12-31 11:38 ./usr/share/man/man1/
-rw-r--r-- root/root 1472 2021-12-31 11:38 ./usr/share/man/man1/racon.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 37916
Build-Time: 1226
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 195
Job: racon_1.5.0-2
Machine Architecture: armhf
Package: racon
Package-Time: 1439
Source-Version: 1.5.0-2
Space: 37916
Status: successful
Version: 1.5.0-2
--------------------------------------------------------------------------------
Finished at 2022-01-02T07:11:33Z
Build needed 00:23:59, 37916k disk space