racon →
1.5.0-3 →
armhf → 2024-02-15 11:09:44
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| racon 1.5.0-3 (armhf) Thu, 15 Feb 2024 10:45:22 +0000 |
+==============================================================================+
Package: racon
Version: 1.5.0-3
Source Version: 1.5.0-3
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-c41cd789-c946-4c98-955d-ec3d65e92ac1' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.4 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.1 MB]
Fetched 29.6 MB in 10s (2946 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: '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 trixie-staging/main racon 1.5.0-3 (dsc) [2106 B]
Get:2 http://172.17.4.1/private trixie-staging/main racon 1.5.0-3 (tar) [3084 kB]
Get:3 http://172.17.4.1/private trixie-staging/main racon 1.5.0-3 (diff) [20.7 kB]
Fetched 3107 kB in 0s (8407 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/racon-erVEZ8/racon-1.5.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/racon-erVEZ8' 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-HekRZe/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-HekRZe/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-HekRZe/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-HekRZe/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-HekRZe/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-HekRZe/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-HekRZe/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-HekRZe/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (10.4 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:
krb5-locales libpam-cap netbase sgml-base util-linux-extra
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 29 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-HekRZe/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 (80.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12880 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-HekRZe/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-HekRZe/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-HekRZe/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-HekRZe/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-HekRZe/apt_archive ./ Sources [558 B]
Get:5 copy:/<<BUILDDIR>>/resolver-HekRZe/apt_archive ./ Packages [644 B]
Fetched 2535 B in 0s (14.1 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 packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
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 libbiosoup-dev libbrotli1 libcereal-dev
libcurl4 libdebhelper-perl libedlib-dev libedlib1 libelf1 libexpat1
libfile-stripnondeterminism-perl libgtest-dev libicu72 libjsoncpp25
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libproc2-0 libpsl5
librhash0 librtmp1 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 cmake-format
elpa-cmake-mode 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 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 libbiosoup-dev libbrotli1 libcereal-dev
libcurl4 libdebhelper-perl libedlib-dev libedlib1 libelf1 libexpat1
libfile-stripnondeterminism-perl libgtest-dev libicu72 libjsoncpp25
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libproc2-0 libpsl5
librhash0 librtmp1 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, 58 newly installed, 0 to remove and 29 not upgraded.
Need to get 32.7 MB of archives.
After this operation, 125 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-HekRZe/apt_archive ./ sbuild-build-depends-racon-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-6 [81.4 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-3 [1358 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libproc2-0 armhf 2:4.0.4-4 [54.8 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf procps armhf 2:4.0.4-4 [848 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libarchive13 armhf 3.7.2-1 [294 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.59.0-1 [61.9 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-4 [195 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libcurl4 armhf 8.5.0-2+rpi1 [377 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf libjsoncpp25 armhf 1.9.5-6 [64.7 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf libuv1 armhf 1.46.0-3+rpi1 [129 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf cmake-data all 3.28.3-1 [2128 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf cmake armhf 3.28.3-1 [7765 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.13 [85.0 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.13 [889 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf googletest all 1.14.0-1+rpi1 [512 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libbiosoup-dev all 0.10.0-4 [7784 B]
Get:48 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.3.dfsg-3 [903 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libbioparser-dev all 3.0.15-3 [9032 B]
Get:50 http://172.17.4.1/private trixie-staging/main armhf rapidjson-dev all 1.1.0+dfsg2-7.1 [97.7 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libcereal-dev armhf 1.3.2+dfsg-4+rpi1 [221 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf libedlib1 armhf 1.2.7-4+b1 [14.4 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf libedlib-dev armhf 1.2.7-4+b1 [19.3 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libgtest-dev armhf 1.14.0-1+rpi1 [236 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libspoa7.0.0 armhf 4.0.8-1 [53.4 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libspoa-dev armhf 4.0.8-1 [9348 B]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libthread-pool-dev armhf 4.0.0-2 [7304 B]
Get:58 http://172.17.4.1/private trixie-staging/main armhf rampler armhf 2.1.1-1 [18.7 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libbrotli1:armhf (1.1.0-2) ...
Setting up libnghttp2-14:armhf (1.59.0-1) ...
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Setting up gettext-base (0.21-14) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-2) ...
Setting up googletest (1.14.0-1+rpi1) ...
Setting up rapidjson-dev (1.1.0+dfsg2-7.1) ...
Setting up libbiosoup-dev (0.10.0-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libuv1:armhf (1.46.0-3+rpi1) ...
Setting up rampler (2.1.1-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libproc2-0:armhf (2:4.0.4-4) ...
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Setting up libspoa7.0.0:armhf (4.0.8-1) ...
Setting up autopoint (0.21-14) ...
Setting up libjsoncpp25:armhf (1.9.5-6) ...
Setting up autoconf (2.71-3) ...
Setting up zlib1g-dev:armhf (1:1.3.dfsg-3) ...
Setting up libedlib1:armhf (1.2.7-4+b1) ...
Setting up libbioparser-dev (3.0.15-3) ...
Setting up librhash0:armhf (1.4.3-3) ...
Setting up libuchardet0:armhf (0.0.8-1) ...
Setting up procps (2:4.0.4-4) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libssh2-1:armhf (1.11.0-4) ...
Setting up cmake-data (3.28.3-1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-14) ...
Setting up libgtest-dev:armhf (1.14.0-1+rpi1) ...
Setting up libtool (2.4.7-7) ...
Setting up libarchive13:armhf (3.7.2-1) ...
Setting up libcereal-dev (1.3.2+dfsg-4+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libedlib-dev:armhf (1.2.7-4+b1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up libcurl4:armhf (8.5.0-2+rpi1) ...
Setting up libspoa-dev:armhf (4.0.8-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.12.0-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up cmake (3.28.3-1) ...
Setting up debhelper (13.13) ...
Setting up sbuild-build-depends-racon-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-13+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.2+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 libc6-dev_2.37-13+rpi1 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 linux-libc-dev_6.5.6-1+rpi1+b1
Package versions: adduser_3.137 apt_2.7.9 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 cmake_3.28.3-1 cmake-data_3.28.3-1 coreutils_9.4-3 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-9+rpi1 dash_0.5.12-6 debconf_1.5.83 debhelper_13.13 debianutils_5.16 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.2+rpi1 dpkg-dev_1.22.2+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc_4:13.2.0-1+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 gcc-13-base_13.2.0-9+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_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 googletest_1.14.0-1+rpi1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-5 libacl1_2.3.1-6 libapt-pkg6.0_2.7.9 libarchive-zip-perl_1.68-1 libarchive13_3.7.2-1 libasan8_13.2.0-9+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-9+rpi1 libattr1_1:2.5.1-5 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41-6+rpi1 libbioparser-dev_3.0.15-3 libbiosoup-dev_0.10.0-4 libblkid1_2.39.3-6 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-13+rpi1 libc-dev-bin_2.37-13+rpi1 libc6_2.37-13+rpi1 libc6-dev_2.37-13+rpi1 libcap-ng0_0.8.4-1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_13.2.0-9+rpi1 libcereal-dev_1.3.2+dfsg-4+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcurl4_8.5.0-2+rpi1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.13 libdpkg-perl_1.22.2+rpi1 libedlib-dev_1.2.7-4+b1 libedlib1_1.2.7-4+b1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.33-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-13+rpi1 libgcc-13-dev_13.2.0-9+rpi1 libgcc-s1_13.2.0-9+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.3-1 libgomp1_13.2.0-9+rpi1 libgpg-error0_1.47-3 libgssapi-krb5-2_1.20.1-5 libgtest-dev_1.14.0-1+rpi1 libhogweed6_3.9.1-2 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libjsoncpp25_1.9.5-6 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1+b1 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-2 libmount1_2.39.3-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20240113-1 libnettle8_3.9.1-2 libnghttp2-14_1.59.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-4 libpam-cap_1:2.66-4 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1 libproc2-0_2:4.0.4-4 libpsl5_0.21.2-1+b1 libreadline8_8.2-3 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2+rpi1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol1_3.1-1 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.3-6 libspoa-dev_4.0.8-1 libspoa7.0.0_4.0.8-1 libsqlite3-0_3.44.2-1 libss2_1.47.0-2 libssh2-1_1.11.0-4 libssl1.1_1.1.1o-1 libssl3_3.1.4-2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libthread-pool-dev_4.0.0-2 libtinfo6_6.4+20240113-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-9+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-6 libuv1_1.46.0-3+rpi1 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1+b1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-3 mawk_1.3.4.20231126-1 mount_2.39.3-6 nano_7.2-2 ncurses-base_6.4+20240113-1 ncurses-bin_6.4+20240113-1 netbase_6.4 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3 po-debconf_1.0.21+nmu1 procps_2:4.0.4-4 rampler_2.1.1-1 rapidjson-dev_1.1.0+dfsg2-7.1 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-racon-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.20 sgml-base_1.31 sysvinit-utils_3.08-5 tar_1.35+dfsg-3 tzdata_2023d-1 usrmerge_38 util-linux_2.39.3-6 util-linux-extra_2.39.3-6 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3 zlib1g-dev_1:1.3.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: Signature made Thu Sep 29 12:45:21 2022 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./racon_1.5.0-3.dsc: no acceptable signature found
dpkg-source: info: extracting racon in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking racon_1.5.0.orig.tar.gz
dpkg-source: info: unpacking racon_1.5.0-3.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
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=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-c41cd789-c946-4c98-955d-ec3d65e92ac1
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package racon
dpkg-buildpackage: info: source version 1.5.0-3
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 && DEB_PYTHON_INSTALL_LAYOUT=deb 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 -DFETCHCONTENT_FULLY_DISCONNECTED=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 13.2.0
-- 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 (1.9s)
-- Generating done (0.0s)
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="
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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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| ~~^ ~~~
| | |
| long unsigned int uint64_t {aka long long unsigned int}
| %llu
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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 (16 ms total)
[----------] 10 tests from RaconPolishingTest
[ RUN ] RaconPolishingTest.ConsensusWithQualities
[racon::Polisher::initialize] loaded target sequences 0.001101 s
[racon::Polisher::initialize] loaded sequences 0.091028 s
[racon::Polisher::initialize] loaded overlaps 0.000769 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.052184 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.078666 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.113695 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.138678 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.171949 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.201353 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.272152 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.307315 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.335636 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.360375 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.395353 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.425504 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.458027 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.474900 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.496977 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.541027 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.558775 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.585320 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.622019 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.658913 s
[racon::Polisher::initialize] transformed data into windows 0.008399 s
[racon::Polisher::polish] generating consensus [=> ] 0.506154 s
[racon::Polisher::polish] generating consensus [==> ] 0.969393 s
[racon::Polisher::polish] generating consensus [===> ] 1.343462 s
[racon::Polisher::polish] generating consensus [====> ] 1.640602 s
[racon::Polisher::polish] generating consensus [=====> ] 1.786346 s
[racon::Polisher::polish] generating consensus [======> ] 1.979378 s
[racon::Polisher::polish] generating consensus [=======> ] 2.167786 s
[racon::Polisher::polish] generating consensus [========> ] 2.369232 s
[racon::Polisher::polish] generating consensus [=========> ] 2.651144 s
[racon::Polisher::polish] generating consensus [==========> ] 3.036788 s
[racon::Polisher::polish] generating consensus [===========> ] 3.582976 s
[racon::Polisher::polish] generating consensus [============> ] 4.235394 s
[racon::Polisher::polish] generating consensus [=============> ] 5.183946 s
[racon::Polisher::polish] generating consensus [==============> ] 6.148349 s
[racon::Polisher::polish] generating consensus [===============> ] 6.798337 s
[racon::Polisher::polish] generating consensus [================> ] 7.274964 s
[racon::Polisher::polish] generating consensus [=================> ] 7.848693 s
[racon::Polisher::polish] generating consensus [==================> ] 8.192680 s
[racon::Polisher::polish] generating consensus [===================>] 8.652681 s
[racon::Polisher::polish] generating consensus [====================] 10.595751 s
[racon::Polisher::] total = 11.391560 s
[ OK ] RaconPolishingTest.ConsensusWithQualities (11401 ms)
[ RUN ] RaconPolishingTest.ConsensusWithoutQualities
[racon::Polisher::initialize] loaded target sequences 0.001013 s
[racon::Polisher::initialize] loaded sequences 0.034369 s
[racon::Polisher::initialize] loaded overlaps 0.000718 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.052040 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.079049 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.111824 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.136927 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.169279 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.198223 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.267783 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.303350 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.331639 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.356253 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.390600 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.420285 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.452855 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.469197 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.490911 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.546486 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.564030 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.591000 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.628642 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.654961 s
[racon::Polisher::initialize] transformed data into windows 0.001121 s
[racon::Polisher::polish] generating consensus [=> ] 0.535103 s
[racon::Polisher::polish] generating consensus [==> ] 1.154096 s
[racon::Polisher::polish] generating consensus [===> ] 1.633778 s
[racon::Polisher::polish] generating consensus [====> ] 1.990567 s
[racon::Polisher::polish] generating consensus [=====> ] 2.218543 s
[racon::Polisher::polish] generating consensus [======> ] 2.476135 s
[racon::Polisher::polish] generating consensus [=======> ] 2.722630 s
[racon::Polisher::polish] generating consensus [========> ] 2.978704 s
[racon::Polisher::polish] generating consensus [=========> ] 3.370091 s
[racon::Polisher::polish] generating consensus [==========> ] 4.014017 s
[racon::Polisher::polish] generating consensus [===========> ] 4.702496 s
[racon::Polisher::polish] generating consensus [============> ] 5.534025 s
[racon::Polisher::polish] generating consensus [=============> ] 6.738260 s
[racon::Polisher::polish] generating consensus [==============> ] 7.622103 s
[racon::Polisher::polish] generating consensus [===============> ] 8.506422 s
[racon::Polisher::polish] generating consensus [================> ] 9.295486 s
[racon::Polisher::polish] generating consensus [=================> ] 10.091687 s
[racon::Polisher::polish] generating consensus [==================> ] 10.586333 s
[racon::Polisher::polish] generating consensus [===================>] 11.143441 s
[racon::Polisher::polish] generating consensus [====================] 14.389836 s
[racon::Polisher::] total = 15.112982 s
[ OK ] RaconPolishingTest.ConsensusWithoutQualities (15123 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments
[racon::Polisher::initialize] loaded target sequences 0.000968 s
[racon::Polisher::initialize] loaded sequences 0.084864 s
[racon::Polisher::initialize] loaded overlaps 0.040557 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.005843 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.006121 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.006381 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.006866 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.007114 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.007396 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.007799 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.008364 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.008607 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.008853 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.009226 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.009765 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.010005 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.010247 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.010479 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.010506 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.010526 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.010545 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.010563 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.010582 s
[racon::Polisher::initialize] transformed data into windows 0.007770 s
[racon::Polisher::polish] generating consensus [=> ] 0.518514 s
[racon::Polisher::polish] generating consensus [==> ] 0.990302 s
[racon::Polisher::polish] generating consensus [===> ] 1.341552 s
[racon::Polisher::polish] generating consensus [====> ] 1.649104 s
[racon::Polisher::polish] generating consensus [=====> ] 1.786430 s
[racon::Polisher::polish] generating consensus [======> ] 1.943437 s
[racon::Polisher::polish] generating consensus [=======> ] 2.140489 s
[racon::Polisher::polish] generating consensus [========> ] 2.358509 s
[racon::Polisher::polish] generating consensus [=========> ] 2.595271 s
[racon::Polisher::polish] generating consensus [==========> ] 2.990634 s
[racon::Polisher::polish] generating consensus [===========> ] 3.532354 s
[racon::Polisher::polish] generating consensus [============> ] 4.097843 s
[racon::Polisher::polish] generating consensus [=============> ] 4.992581 s
[racon::Polisher::polish] generating consensus [==============> ] 5.937851 s
[racon::Polisher::polish] generating consensus [===============> ] 6.653791 s
[racon::Polisher::polish] generating consensus [================> ] 7.147596 s
[racon::Polisher::polish] generating consensus [=================> ] 7.748679 s
[racon::Polisher::polish] generating consensus [==================> ] 8.118934 s
[racon::Polisher::polish] generating consensus [===================>] 8.467477 s
[racon::Polisher::polish] generating consensus [====================] 10.103192 s
[racon::Polisher::] total = 10.280978 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments (10290 ms)
[ RUN ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments
[racon::Polisher::initialize] loaded target sequences 0.000951 s
[racon::Polisher::initialize] loaded sequences 0.030628 s
[racon::Polisher::initialize] loaded overlaps 0.040379 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.003275 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.003500 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.003762 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.004043 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.004201 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.004376 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.004636 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.005096 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.005241 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.005413 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.005666 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.006100 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.006262 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.006553 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.006854 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.007230 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.007370 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.007479 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.007658 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.007707 s
[racon::Polisher::initialize] transformed data into windows 0.000891 s
[racon::Polisher::polish] generating consensus [=> ] 0.492526 s
[racon::Polisher::polish] generating consensus [==> ] 1.038599 s
[racon::Polisher::polish] generating consensus [===> ] 1.468314 s
[racon::Polisher::polish] generating consensus [====> ] 1.795464 s
[racon::Polisher::polish] generating consensus [=====> ] 2.026770 s
[racon::Polisher::polish] generating consensus [======> ] 2.248050 s
[racon::Polisher::polish] generating consensus [=======> ] 2.477296 s
[racon::Polisher::polish] generating consensus [========> ] 2.792804 s
[racon::Polisher::polish] generating consensus [=========> ] 3.108814 s
[racon::Polisher::polish] generating consensus [==========> ] 3.591512 s
[racon::Polisher::polish] generating consensus [===========> ] 4.213800 s
[racon::Polisher::polish] generating consensus [============> ] 4.984335 s
[racon::Polisher::polish] generating consensus [=============> ] 6.011577 s
[racon::Polisher::polish] generating consensus [==============> ] 7.005910 s
[racon::Polisher::polish] generating consensus [===============> ] 7.914571 s
[racon::Polisher::polish] generating consensus [================> ] 8.720293 s
[racon::Polisher::polish] generating consensus [=================> ] 9.455611 s
[racon::Polisher::polish] generating consensus [==================> ] 9.890611 s
[racon::Polisher::polish] generating consensus [===================>] 10.367945 s
[racon::Polisher::polish] generating consensus [====================] 13.107069 s
[racon::Polisher::] total = 13.211800 s
[ OK ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments (13221 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow
[racon::Polisher::initialize] loaded target sequences 0.000946 s
[racon::Polisher::initialize] loaded sequences 0.084978 s
[racon::Polisher::initialize] loaded overlaps 0.000675 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.048192 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.074907 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.110666 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.135464 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.167841 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.197389 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.265778 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.299905 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.327641 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.352341 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.386143 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.415305 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.447209 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.463204 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.484553 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.525842 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.542076 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.568153 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.611442 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.651312 s
[racon::Polisher::initialize] transformed data into windows 0.007773 s
[racon::Polisher::polish] generating consensus [=> ] 1.802168 s
[racon::Polisher::polish] generating consensus [==> ] 1.802224 s
[racon::Polisher::polish] generating consensus [===> ] 3.360582 s
[racon::Polisher::polish] generating consensus [====> ] 3.360655 s
[racon::Polisher::polish] generating consensus [=====> ] 4.107073 s
[racon::Polisher::polish] generating consensus [======> ] 4.107126 s
[racon::Polisher::polish] generating consensus [=======> ] 4.698113 s
[racon::Polisher::polish] generating consensus [========> ] 4.698182 s
[racon::Polisher::polish] generating consensus [=========> ] 5.819416 s
[racon::Polisher::polish] generating consensus [==========> ] 5.872593 s
[racon::Polisher::polish] generating consensus [===========> ] 7.896030 s
[racon::Polisher::polish] generating consensus [============> ] 8.129256 s
[racon::Polisher::polish] generating consensus [=============> ] 11.137904 s
[racon::Polisher::polish] generating consensus [==============> ] 11.879208 s
[racon::Polisher::polish] generating consensus [===============> ] 13.473849 s
[racon::Polisher::polish] generating consensus [================> ] 14.003059 s
[racon::Polisher::polish] generating consensus [=================> ] 15.503991 s
[racon::Polisher::polish] generating consensus [==================> ] 15.952428 s
[racon::Polisher::polish] generating consensus [===================>] 17.047000 s
[racon::Polisher::polish] generating consensus [====================] 21.110433 s
[racon::Polisher::] total = 21.896121 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow (21913 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesEditDistance
[racon::Polisher::initialize] loaded target sequences 0.000993 s
[racon::Polisher::initialize] loaded sequences 0.089408 s
[racon::Polisher::initialize] loaded overlaps 0.000700 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.052492 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.081447 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.119694 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.145698 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.181622 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.213231 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.284219 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.321260 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.349916 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.375074 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.410506 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.468129 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.485855 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.524486 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.571749 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.650944 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.660299 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.670163 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.688412 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.695106 s
[racon::Polisher::initialize] transformed data into windows 0.008652 s
[racon::Polisher::polish] generating consensus [=> ] 0.588895 s
[racon::Polisher::polish] generating consensus [==> ] 1.045377 s
[racon::Polisher::polish] generating consensus [===> ] 1.407070 s
[racon::Polisher::polish] generating consensus [====> ] 1.697374 s
[racon::Polisher::polish] generating consensus [=====> ] 1.834572 s
[racon::Polisher::polish] generating consensus [======> ] 2.019346 s
[racon::Polisher::polish] generating consensus [=======> ] 2.198184 s
[racon::Polisher::polish] generating consensus [========> ] 2.398592 s
[racon::Polisher::polish] generating consensus [=========> ] 2.695192 s
[racon::Polisher::polish] generating consensus [==========> ] 3.109262 s
[racon::Polisher::polish] generating consensus [===========> ] 3.612709 s
[racon::Polisher::polish] generating consensus [============> ] 4.431049 s
[racon::Polisher::polish] generating consensus [=============> ] 5.428810 s
[racon::Polisher::polish] generating consensus [==============> ] 6.576073 s
[racon::Polisher::polish] generating consensus [===============> ] 7.346624 s
[racon::Polisher::polish] generating consensus [================> ] 7.801658 s
[racon::Polisher::polish] generating consensus [=================> ] 8.364720 s
[racon::Polisher::polish] generating consensus [==================> ] 8.699611 s
[racon::Polisher::polish] generating consensus [===================>] 9.173354 s
[racon::Polisher::polish] generating consensus [====================] 10.795490 s
[racon::Polisher::] total = 11.623645 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesEditDistance (11633 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualities
[racon::Polisher::initialize] loaded target sequences 0.086125 s
[racon::Polisher::initialize] loaded sequences 0.088351 s
[racon::Polisher::initialize] loaded overlaps 0.023373 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.082686 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.130444 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.152891 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.181619 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.215494 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.246335 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.298131 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.328267 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.373446 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.410955 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.450624 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.514786 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.558728 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.608148 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.645232 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.695939 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.741362 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.761411 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.783692 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.816902 s
[racon::Polisher::initialize] transformed data into windows 0.013398 s
[racon::Polisher::polish] generating consensus [=> ] 0.482101 s
[racon::Polisher::polish] generating consensus [==> ] 1.234175 s
[racon::Polisher::polish] generating consensus [===> ] 1.937768 s
[racon::Polisher::polish] generating consensus [====> ] 1.938941 s
[racon::Polisher::polish] generating consensus [=====> ] 2.251861 s
[racon::Polisher::polish] generating consensus [======> ] 2.390702 s
[racon::Polisher::polish] generating consensus [=======> ] 2.629947 s
[racon::Polisher::polish] generating consensus [========> ] 2.634917 s
[racon::Polisher::polish] generating consensus [=========> ] 3.211188 s
[racon::Polisher::polish] generating consensus [==========> ] 3.426445 s
[racon::Polisher::polish] generating consensus [===========> ] 3.570686 s
[racon::Polisher::polish] generating consensus [============> ] 3.620008 s
[racon::Polisher::polish] generating consensus [=============> ] 3.806678 s
[racon::Polisher::polish] generating consensus [==============> ] 3.808059 s
[racon::Polisher::polish] generating consensus [===============> ] 4.223876 s
[racon::Polisher::polish] generating consensus [================> ] 4.225376 s
[racon::Polisher::polish] generating consensus [=================> ] 5.009288 s
[racon::Polisher::polish] generating consensus [==================> ] 5.295410 s
[racon::Polisher::polish] generating consensus [===================>] 5.388439 s
[racon::Polisher::polish] generating consensus [====================] 5.426993 s
[racon::Polisher::] total = 6.456675 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualities (6465 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull
[racon::Polisher::initialize] loaded target sequences 0.089985 s
[racon::Polisher::initialize] loaded sequences 0.092349 s
[racon::Polisher::initialize] loaded overlaps 0.023824 s
[racon::Polisher::initialize] aligning overlaps [=> ] 1.017571 s
[racon::Polisher::initialize] aligning overlaps [==> ] 1.584320 s
[racon::Polisher::initialize] aligning overlaps [===> ] 2.139931 s
[racon::Polisher::initialize] aligning overlaps [====> ] 2.865574 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 3.389255 s
[racon::Polisher::initialize] aligning overlaps [======> ] 3.845396 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 4.443020 s
[racon::Polisher::initialize] aligning overlaps [========> ] 5.224462 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 6.003938 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 6.662568 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 7.219161 s
[racon::Polisher::initialize] aligning overlaps [============> ] 8.011035 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 8.878066 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 9.616236 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 10.494171 s
[racon::Polisher::initialize] aligning overlaps [================> ] 11.313589 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 12.003084 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 12.876031 s
[racon::Polisher::initialize] aligning overlaps [===================>] 13.770367 s
[racon::Polisher::initialize] aligning overlaps [====================] 14.335966 s
[racon::Polisher::initialize] transformed data into windows 0.220743 s
[racon::Polisher::polish] generating consensus [=> ] 17.596936 s
[racon::Polisher::polish] generating consensus [==> ] 30.156744 s
[racon::Polisher::polish] generating consensus [===> ] 43.759862 s
[racon::Polisher::polish] generating consensus [====> ] 55.188249 s
[racon::Polisher::polish] generating consensus [=====> ] 67.323383 s
[racon::Polisher::polish] generating consensus [======> ] 81.988622 s
[racon::Polisher::polish] generating consensus [=======> ] 96.520457 s
[racon::Polisher::polish] generating consensus [========> ] 107.004684 s
[racon::Polisher::polish] generating consensus [=========> ] 120.347399 s
[racon::Polisher::polish] generating consensus [==========> ] 136.239396 s
[racon::Polisher::polish] generating consensus [===========> ] 149.138677 s
[racon::Polisher::polish] generating consensus [============> ] 163.900542 s
[racon::Polisher::polish] generating consensus [=============> ] 176.824707 s
[racon::Polisher::polish] generating consensus [==============> ] 190.500234 s
[racon::Polisher::polish] generating consensus [===============> ] 205.618461 s
[racon::Polisher::polish] generating consensus [================> ] 213.850773 s
[racon::Polisher::polish] generating consensus [=================> ] 230.331636 s
[racon::Polisher::polish] generating consensus [==================> ] 245.791093 s
[racon::Polisher::polish] generating consensus [===================>] 260.622969 s
[racon::Polisher::polish] generating consensus [====================] 272.634023 s
[racon::Polisher::] total = 287.404800 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull (287415 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull
[racon::Polisher::initialize] loaded target sequences 0.031644 s
[racon::Polisher::initialize] loaded sequences 0.032024 s
[racon::Polisher::initialize] loaded overlaps 0.023286 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.817357 s
[racon::Polisher::initialize] aligning overlaps [==> ] 1.373443 s
[racon::Polisher::initialize] aligning overlaps [===> ] 1.913401 s
[racon::Polisher::initialize] aligning overlaps [====> ] 2.673395 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 3.310191 s
[racon::Polisher::initialize] aligning overlaps [======> ] 3.774495 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 4.378886 s
[racon::Polisher::initialize] aligning overlaps [========> ] 5.164065 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 5.882625 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 6.600301 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 7.151023 s
[racon::Polisher::initialize] aligning overlaps [============> ] 7.934095 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 8.730987 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 9.384902 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 10.294619 s
[racon::Polisher::initialize] aligning overlaps [================> ] 11.124918 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 11.850591 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 12.637201 s
[racon::Polisher::initialize] aligning overlaps [===================>] 13.539014 s
[racon::Polisher::initialize] aligning overlaps [====================] 14.241084 s
[racon::Polisher::initialize] transformed data into windows 0.039982 s
[racon::Polisher::polish] generating consensus [=> ] 23.696982 s
[racon::Polisher::polish] generating consensus [==> ] 42.533968 s
[racon::Polisher::polish] generating consensus [===> ] 61.268764 s
[racon::Polisher::polish] generating consensus [====> ] 75.317585 s
[racon::Polisher::polish] generating consensus [=====> ] 91.925183 s
[racon::Polisher::polish] generating consensus [======> ] 110.593604 s
[racon::Polisher::polish] generating consensus [=======> ] 130.738385 s
[racon::Polisher::polish] generating consensus [========> ] 145.455693 s
[racon::Polisher::polish] generating consensus [=========> ] 164.189887 s
[racon::Polisher::polish] generating consensus [==========> ] 186.053110 s
[racon::Polisher::polish] generating consensus [===========> ] 203.850569 s
[racon::Polisher::polish] generating consensus [============> ] 224.471193 s
[racon::Polisher::polish] generating consensus [=============> ] 244.190418 s
[racon::Polisher::polish] generating consensus [==============> ] 263.508551 s
[racon::Polisher::polish] generating consensus [===============> ] 283.016617 s
[racon::Polisher::polish] generating consensus [================> ] 293.593002 s
[racon::Polisher::polish] generating consensus [=================> ] 317.839985 s
[racon::Polisher::polish] generating consensus [==================> ] 340.887170 s
[racon::Polisher::polish] generating consensus [===================>] 360.092238 s
[racon::Polisher::polish] generating consensus [====================] 377.821964 s
[racon::Polisher::] total = 392.197649 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull (392207 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap
[racon::Polisher::initialize] loaded target sequences 0.084207 s
[racon::Polisher::initialize] loaded sequences 0.084549 s
[racon::Polisher::initialize] loaded overlaps 0.020253 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.820298 s
[racon::Polisher::initialize] aligning overlaps [==> ] 1.363748 s
[racon::Polisher::initialize] aligning overlaps [===> ] 1.863866 s
[racon::Polisher::initialize] aligning overlaps [====> ] 2.587764 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 3.219590 s
[racon::Polisher::initialize] aligning overlaps [======> ] 3.664888 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 4.274414 s
[racon::Polisher::initialize] aligning overlaps [========> ] 5.039894 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 5.745835 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 6.453899 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 6.998054 s
[racon::Polisher::initialize] aligning overlaps [============> ] 7.771013 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 8.553622 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 9.216292 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 10.101411 s
[racon::Polisher::initialize] aligning overlaps [================> ] 10.932387 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 11.654749 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 12.458493 s
[racon::Polisher::initialize] aligning overlaps [===================>] 13.347162 s
[racon::Polisher::initialize] aligning overlaps [====================] 14.026791 s
[racon::Polisher::initialize] transformed data into windows 0.216531 s
[racon::Polisher::polish] generating consensus [=> ] 17.049771 s
[racon::Polisher::polish] generating consensus [==> ] 29.140568 s
[racon::Polisher::polish] generating consensus [===> ] 42.496281 s
[racon::Polisher::polish] generating consensus [====> ] 53.527103 s
[racon::Polisher::polish] generating consensus [=====> ] 65.210075 s
[racon::Polisher::polish] generating consensus [======> ] 79.155481 s
[racon::Polisher::polish] generating consensus [=======> ] 93.403751 s
[racon::Polisher::polish] generating consensus [========> ] 103.668553 s
[racon::Polisher::polish] generating consensus [=========> ] 116.703059 s
[racon::Polisher::polish] generating consensus [==========> ] 132.226612 s
[racon::Polisher::polish] generating consensus [===========> ] 144.808053 s
[racon::Polisher::polish] generating consensus [============> ] 159.233194 s
[racon::Polisher::polish] generating consensus [=============> ] 171.861140 s
[racon::Polisher::polish] generating consensus [==============> ] 185.364952 s
[racon::Polisher::polish] generating consensus [===============> ] 199.976848 s
[racon::Polisher::polish] generating consensus [================> ] 207.948816 s
[racon::Polisher::polish] generating consensus [=================> ] 223.901004 s
[racon::Polisher::polish] generating consensus [==================> ] 238.889697 s
[racon::Polisher::polish] generating consensus [===================>] 253.223782 s
[racon::Polisher::polish] generating consensus [====================] 264.575453 s
[racon::Polisher::] total = 279.015322 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap (279024 ms)
[----------] 10 tests from RaconPolishingTest (1048696 ms total)
[----------] Global test environment tear-down
[==========] 15 tests from 2 test suites ran. (1048712 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' in '../racon_1.5.0-3_armhf.deb'.
dpkg-deb: building package 'racon-dbgsym' in '../racon-dbgsym_1.5.0-3_armhf.deb'.
dpkg-genbuildinfo --build=any -O../racon_1.5.0-3_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../racon_1.5.0-3_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 2024-02-15T11:09:41Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
racon_1.5.0-3_armhf.changes:
----------------------------
Format: 1.8
Date: Thu, 29 Sep 2022 14:39:55 +0200
Source: racon
Binary: racon racon-dbgsym
Architecture: armhf
Version: 1.5.0-3
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <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 (1.5.0-3) unstable; urgency=medium
.
* Standards-Version: 4.6.1 (routine-update)
* Drop patch making racon compatible to old libthread_pool
Checksums-Sha1:
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2317eb25ee5f0a3d7da03706b8da0a2db2893586 6246 racon_1.5.0-3_armhf.buildinfo
2948f672b7df994891b767d2d098011c34f26b3c 3104136 racon_1.5.0-3_armhf.deb
Checksums-Sha256:
cbb93772ba9a44c80a96049158c1cda0e76d2fce0d6192cfc82ac446d05aa60b 987888 racon-dbgsym_1.5.0-3_armhf.deb
d7880467448200cbd7a794c471296392799424506600e37749a9ce562af4b1ee 6246 racon_1.5.0-3_armhf.buildinfo
1a5c4c78c3840994ffd19310b800db4c63ffc7943317b35a7f88d93b37aacc7a 3104136 racon_1.5.0-3_armhf.deb
Files:
109ca29466f9c399a98f0fdff3b182fa 987888 debug optional racon-dbgsym_1.5.0-3_armhf.deb
ce3a6d605544ed2022af68419ec14ef5 6246 science optional racon_1.5.0-3_armhf.buildinfo
aaadee072eab17dae437f47fab42d933 3104136 science optional racon_1.5.0-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
racon-dbgsym_1.5.0-3_armhf.deb
------------------------------
new Debian package, version 2.0.
size 987888 bytes: control archive=532 bytes.
363 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: racon-dbgsym
Source: racon
Version: 1.5.0-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1038
Depends: racon (= 1.5.0-3)
Section: debug
Priority: optional
Description: debug symbols for racon
Build-Ids: 95ba35ed1e5f4a455658e170bf222621eee9ffc5
drwxr-xr-x root/root 0 2022-09-29 12:39 ./
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/lib/
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/lib/debug/.build-id/95/
-rw-r--r-- root/root 1052292 2022-09-29 12:39 ./usr/lib/debug/.build-id/95/ba35ed1e5f4a455658e170bf222621eee9ffc5.debug
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/share/
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-09-29 12:39 ./usr/share/doc/racon-dbgsym -> racon
racon_1.5.0-3_armhf.deb
-----------------------
new Debian package, version 2.0.
size 3104136 bytes: control archive=1852 bytes.
2118 bytes, 41 lines control
1249 bytes, 16 lines md5sums
Package: racon
Version: 1.5.0-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3138
Depends: libc6 (>= 2.34), libedlib1 (>= 1.2.7-3~), libgcc-s1 (>= 3.5), libspoa7.0.0 (>= 4.0.8), libstdc++6 (>= 13.1), 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 2022-09-29 12:39 ./
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/bin/
-rwxr-xr-x root/root 128728 2022-09-29 12:39 ./usr/bin/racon
-rwxr-xr-x root/root 10415 2022-09-29 12:39 ./usr/bin/racon_wrapper.py
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/share/
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/share/doc/racon/
-rw-r--r-- root/root 278 2022-09-29 12:39 ./usr/share/doc/racon/README.test
-rw-r--r-- root/root 1215 2022-09-29 12:39 ./usr/share/doc/racon/changelog.Debian.gz
-rw-r--r-- root/root 1647 2022-09-29 12:39 ./usr/share/doc/racon/copyright
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/share/doc/racon/examples/
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/share/doc/racon/examples/data/
-rw-r--r-- root/root 146882 2022-09-29 12:39 ./usr/share/doc/racon/examples/data/sample_ava_overlaps.mhap.gz
-rw-r--r-- root/root 151632 2022-09-29 12:39 ./usr/share/doc/racon/examples/data/sample_ava_overlaps.paf.gz
-rw-r--r-- root/root 14197 2022-09-29 12:39 ./usr/share/doc/racon/examples/data/sample_layout.fasta.gz
-rw-r--r-- root/root 5111 2022-09-29 12:39 ./usr/share/doc/racon/examples/data/sample_overlaps.paf.gz
-rw-r--r-- root/root 698977 2022-09-29 12:39 ./usr/share/doc/racon/examples/data/sample_overlaps.sam.gz
-rw-r--r-- root/root 488701 2022-09-29 12:39 ./usr/share/doc/racon/examples/data/sample_reads.fasta.gz
-rw-r--r-- root/root 1526281 2022-09-29 12:39 ./usr/share/doc/racon/examples/data/sample_reads.fastq.gz
-rw-r--r-- root/root 15195 2022-09-29 12:39 ./usr/share/doc/racon/examples/data/sample_reference.fasta.gz
-rw-r--r-- root/root 566 2022-09-29 12:39 ./usr/share/doc/racon/run-unit-test
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/share/lintian/
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 114 2022-09-29 12:39 ./usr/share/lintian/overrides/racon
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/share/man/
drwxr-xr-x root/root 0 2022-09-29 12:39 ./usr/share/man/man1/
-rw-r--r-- root/root 1472 2022-09-29 12:39 ./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: 31012
Build-Time: 1107
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 333
Job: racon_1.5.0-3
Machine Architecture: armhf
Package: racon
Package-Time: 1459
Source-Version: 1.5.0-3
Space: 31012
Status: successful
Version: 1.5.0-3
--------------------------------------------------------------------------------
Finished at 2024-02-15T11:09:41Z
Build needed 00:24:19, 31012k disk space