racon →
1.4.20-1 →
armhf → 2021-01-20 01:06:32
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| racon 1.4.20-1 (armhf) Wed, 20 Jan 2021 00:05:14 +0000 |
+==============================================================================+
Package: racon
Version: 1.4.20-1
Source Version: 1.4.20-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-151d2ae3-7d0b-4cd1-bef2-40226960103a' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.1 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.1 MB]
Fetched 25.2 MB in 28s (894 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 3092 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main racon 1.4.20-1 (dsc) [2083 B]
Get:2 http://172.17.0.1/private bullseye-staging/main racon 1.4.20-1 (tar) [3083 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main racon 1.4.20-1 (diff) [6268 B]
Fetched 3092 kB in 1s (2831 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/racon-2aQGpm/racon-1.4.20' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/racon-2aQGpm' 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-dKtzK8/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-dKtzK8/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-dKtzK8/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-dKtzK8/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-dKtzK8/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-dKtzK8/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-dKtzK8/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-dKtzK8/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (2711 B/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:
bsdextrautils krb5-locales libnss-nis libnss-nisplus libpam-cap netbase
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 76 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-dKtzK8/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 (23.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12565 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 (>= 3.0.12), libcereal-dev, libedlib-dev, libspoa-dev, libthread-pool-dev (>= 3.0.2), rampler
Filtered Build-Depends: debhelper-compat (= 13), cmake, libgtest-dev, libbioparser-dev (>= 3.0.12), libcereal-dev, libedlib-dev, libspoa-dev, libthread-pool-dev (>= 3.0.2), rampler
dpkg-deb: building package 'sbuild-build-depends-racon-dummy' in '/<<BUILDDIR>>/resolver-dKtzK8/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-dKtzK8/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-dKtzK8/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-dKtzK8/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-dKtzK8/apt_archive ./ Sources [553 B]
Get:5 copy:/<<BUILDDIR>>/resolver-dKtzK8/apt_archive ./ Packages [637 B]
Fetched 2523 B in 1s (3195 B/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 libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev cmake cmake-data debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
googletest groff-base intltool-debian libarchive-zip-perl libarchive13
libbioparser-dev libbrotli1 libcereal-dev libcurl4 libdebhelper-perl
libedlib-dev libedlib0 libelf1 libexpat1 libfile-stripnondeterminism-perl
libgtest-dev libicu67 libjsoncpp24 libmagic-mgc libmagic1 libncurses6
libncursesw6 libnghttp2-14 libpipeline1 libprocps8 libpsl5 librhash0
librtmp1 libsigsegv2 libspoa-dev libspoa7.0.0 libssh2-1 libsub-override-perl
libthread-pool-dev libtinfo6 libtool libuchardet0 libuv1 libxml2 m4 man-db
po-debconf procps rampler rapidjson-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make
gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl rapidjson-doc
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libgpm2 publicsuffix
libltdl-dev libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev cmake cmake-data debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
googletest groff-base intltool-debian libarchive-zip-perl libarchive13
libbioparser-dev libbrotli1 libcereal-dev libcurl4 libdebhelper-perl
libedlib-dev libedlib0 libelf1 libexpat1 libfile-stripnondeterminism-perl
libgtest-dev libicu67 libjsoncpp24 libmagic-mgc libmagic1 libncurses6
libnghttp2-14 libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2
libspoa-dev libspoa7.0.0 libssh2-1 libsub-override-perl libthread-pool-dev
libtool libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps rampler
rapidjson-dev sbuild-build-depends-racon-dummy zlib1g-dev
The following packages will be upgraded:
libncursesw6 libtinfo6
2 upgraded, 58 newly installed, 0 to remove and 74 not upgraded.
Need to get 27.1 MB of archives.
After this operation, 111 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-dKtzK8/apt_archive ./ sbuild-build-depends-racon-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.2+20201114-2 [328 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.2+20201114-2 [105 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-5 [59.8 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-5 [238 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-3 [170 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-3 [32.4 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-3 [509 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.18.4-1+rpi1 [1725 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.42.0-1 [66.7 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.74.0-1 [305 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp24 armhf 1.9.4-4 [67.0 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.4.1-1 [140 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.40.0-1 [118 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.18.4-1+rpi1+b1 [3111 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.1 [188 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-3 [162 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20201015-2 [162 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-3 [1214 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.1 [1010 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf googletest all 1.10.0.20201025-1.1 [629 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libbioparser-dev all 3.0.12-1 [7168 B]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf rapidjson-dev all 1.1.0+dfsg2-7 [98.9 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libcereal-dev all 1.3.0+dfsg-1 [210 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libedlib0 armhf 1.2.6-1 [13.6 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libedlib-dev armhf 1.2.6-1 [15.9 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libgtest-dev armhf 1.10.0.20201025-1.1 [1388 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libspoa7.0.0 armhf 4.0.6+ds2-2 [51.2 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libspoa-dev armhf 4.0.6+ds2-2 [6708 B]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libthread-pool-dev all 3.0.2-1 [4376 B]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf rampler armhf 1.1.1-3 [18.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libtinfo6:armhf (6.2+20201114-2) ...
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Setting up libpsl5:armhf (0.21.0-1.1) ...
Setting up libicu67:armhf (67.1-6) ...
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Setting up autotools-dev (20180224.1+nmu1) ...
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-2) ...
Setting up libsigsegv2:armhf (2.12-3) ...
Setting up libthread-pool-dev (3.0.2-1) ...
Setting up libspoa7.0.0:armhf (4.0.6+ds2-2) ...
Setting up autopoint (0.21-3) ...
Setting up libedlib0 (1.2.6-1) ...
Setting up libjsoncpp24:armhf (1.9.4-4) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libbioparser-dev (3.0.12-1) ...
Setting up librhash0:armhf (1.4.1-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.9.0-2) ...
Setting up cmake-data (3.18.4-1+rpi1) ...
Setting up libelf1:armhf (0.182-3) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
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Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up gettext (0.21-3) ...
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Setting up libtool (2.4.6-15) ...
Setting up libarchive13:armhf (3.4.3-2) ...
Setting up libcereal-dev (1.3.0+dfsg-1) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libedlib-dev (1.2.6-1) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13+20201015-2) ...
Setting up groff-base (1.22.4-5) ...
Setting up procps (2:3.3.16-5) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
Setting up libcurl4:armhf (7.74.0-1) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libspoa-dev:armhf (4.0.6+ds2-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up cmake (3.18.4-1+rpi1+b1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.3.1) ...
Setting up sbuild-build-depends-racon-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-5+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.1-1+rpi1 gcc-10_10.2.1-1+rpi1 libc6-dev_2.31-5+rpi1 libstdc++-10-dev_10.2.1-1+rpi1 libstdc++6_10.2.1-1+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1
Package versions: adduser_3.118 apt_2.1.12 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-3 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-1 binutils_2.35.1-5+rpi1 binutils-arm-linux-gnueabihf_2.35.1-5+rpi1 binutils-common_2.35.1-5+rpi1 bsdextrautils_2.36.1-2 bsdutils_1:2.36.1-2 build-essential_12.8 bzip2_1.0.8-4 cmake_3.18.4-1+rpi1+b1 cmake-data_3.18.4-1+rpi1 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.1-1+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13+20201015-2 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-2 file_1:5.39-3 findutils_4.7.0+git20201010-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.1-1+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.1-1+rpi1 gcc-10-base_10.2.1-1+rpi1 gettext_0.21-3 gettext-base_0.21-3 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 googletest_1.10.0.20201025-1.1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.18.3-4 libacl1_2.2.53-8 libapt-pkg6.0_2.1.12 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_10.2.1-1+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1+b1 libbinutils_2.35.1-5+rpi1 libbioparser-dev_3.0.12-1 libblkid1_2.36.1-2 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-5+rpi1 libc-dev-bin_2.31-5+rpi1 libc6_2.31-5+rpi1 libc6-dev_2.31-5+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.1-1+rpi1 libcereal-dev_1.3.0+dfsg-1 libcom-err2_1.45.6-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-5+rpi1 libctf0_2.35.1-5+rpi1 libcurl4_7.74.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.255+b1 libdebhelper-perl_13.3.1 libdpkg-perl_1.20.5+rpi1 libedlib-dev_1.2.6-1 libedlib0_1.2.6-1 libelf1_0.182-3 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-2 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.1-1+rpi1 libgcc-s1_10.2.1-1+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.6.15-4 libgomp1_10.2.1-1+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libgtest-dev_1.10.0.20201025-1.1 libhogweed6_3.6-2 libicu67_67.1-6 libidn2-0_2.3.0-4 libisl23_0.23-1 libjsoncpp24_1.9.4-4 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-2 libldap-2.4-2_2.4.56+dfsg-1+rpi1+b1 libldap-common_2.4.56+dfsg-1+rpi1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-2 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libprocps8_2:3.3.16-5 libpsl5_0.21.0-1.1 libreadline8_8.1-1 librhash0_1.4.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 librust-rand-core-dev_0.5.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.0-3+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.12-3 libsmartcols1_2.36.1-2 libspoa-dev_4.0.6+ds2-2 libspoa7.0.0_4.0.6+ds2-2 libsqlite3-0_3.34.0-1 libss2_1.45.6-1 libssh2-1_1.9.0-2 libssl1.1_1.1.1h-1 libstdc++-10-dev_10.2.1-1+rpi1 libstdc++6_10.2.1-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.6-4+rpi1 libtasn1-6_4.16.0-2 libthread-pool-dev_3.0.2-1 libtinfo6_6.2+20201114-2 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-15 libubsan1_10.2.1-1+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-4+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-2 libuv1_1.40.0-1 libxml2_2.9.10+dfsg-6.3 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36.1-2 ncurses-base_6.2+20201114-1 ncurses-bin_6.2+20201114-1 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 procps_2:3.3.16-5 rampler_1.1.1-3 rapidjson-dev_1.1.0+dfsg2-7 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-racon-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2020d-1 util-linux_2.36.1-2 xz-utils_5.2.4-1 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.PY_gL5xm/trustedkeys.kbx': General error
gpgv: Signature made Tue Jan 19 10:04:56 2021 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./racon_1.4.20-1.dsc
dpkg-source: info: extracting racon in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking racon_1.4.20.orig.tar.gz
dpkg-source: info: unpacking racon_1.4.20-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_libs.patch
dpkg-source: info: applying remove_buildpath
dpkg-source: info: applying py3
Check disc 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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-151d2ae3-7d0b-4cd1-bef2-40226960103a
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package racon
dpkg-buildpackage: info: source version 1.4.20-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --buildsystem=cmake
dh_auto_clean -O--buildsystem=cmake
dh_autoreconf_clean -O--buildsystem=cmake
dh_clean -O--buildsystem=cmake
debian/rules binary-arch
dh binary-arch --buildsystem=cmake
dh_update_autotools_config -a -O--buildsystem=cmake
dh_autoreconf -a -O--buildsystem=cmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -Dracon_build_tests=ON -Dracon_build_wrapper=ON
cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -Dracon_build_tests=ON -Dracon_build_wrapper=ON ..
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found GTest: /usr/lib/arm-linux-gnueabihf/libgtest.a
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
# Somehow the means in the patch for CMakeLists.txt to replace -lpthread by -pthread to not work
# Just hack it here
sed -i 's/-lpthread/-pthread/' obj-*/CMakeFiles/racon_test.dir/link.txt
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a -O--buildsystem=cmake
cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/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_test.dir/build.make CMakeFiles/racon_test.dir/depend
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219 | "edlib unable to align pair (%zu x %zu)!\n", q_id_, t_id_);
| ~~^ ~~~~~
| | |
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| %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_);
| ~~^ ~~~~~
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| unsigned int uint64_t {aka long long unsigned int}
| %llu
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219 | "edlib unable to align pair (%zu x %zu)!\n", q_id_, t_id_);
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219 | "edlib unable to align pair (%zu x %zu)!\n", q_id_, t_id_);
| ~~^ ~~~~~
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142 | "contig %lu might be chimeric in window %u!\n", id_, rank_);
| ~~^ ~~~
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142 | "contig %lu might be chimeric in window %u!\n", id_, rank_);
| ~~^ ~~~
| | |
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Running main() from /build/googletest-MTVrzi/googletest-1.10.0.20201025/googletest/src/gtest_main.cc
[==========] Running 15 tests from 2 test suites.
[----------] Global test environment set-up.
[----------] 5 tests from RaconInitializeTest
[ RUN ] RaconInitializeTest.PolisherTypeError
[ OK ] RaconInitializeTest.PolisherTypeError (8 ms)
[ RUN ] RaconInitializeTest.WindowLengthError
[ OK ] RaconInitializeTest.WindowLengthError (8 ms)
[ RUN ] RaconInitializeTest.SequencesPathExtensionError
[ OK ] RaconInitializeTest.SequencesPathExtensionError (10 ms)
[ RUN ] RaconInitializeTest.OverlapsPathExtensionError
[ OK ] RaconInitializeTest.OverlapsPathExtensionError (20 ms)
[ RUN ] RaconInitializeTest.TargetPathExtensionError
[ OK ] RaconInitializeTest.TargetPathExtensionError (21 ms)
[----------] 5 tests from RaconInitializeTest (70 ms total)
[----------] 10 tests from RaconPolishingTest
[ RUN ] RaconPolishingTest.ConsensusWithQualities
[racon::Polisher::initialize] loaded target sequences 0.003707 s
[racon::Polisher::initialize] loaded sequences 0.247517 s
[racon::Polisher::initialize] loaded overlaps 0.002928 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.180681 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.297896 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.373219 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.489886 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.571676 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.639889 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.771987 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.892640 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.982105 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 1.112060 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 1.189414 s
[racon::Polisher::initialize] aligning overlaps [============> ] 1.317086 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 1.474034 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 1.550947 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 1.676573 s
[racon::Polisher::initialize] aligning overlaps [================> ] 1.881804 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 1.957246 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 2.074927 s
[racon::Polisher::initialize] aligning overlaps [===================>] 2.272358 s
[racon::Polisher::initialize] aligning overlaps [====================] 2.378180 s
[racon::Polisher::initialize] transformed data into windows 0.017505 s
[racon::Polisher::polish] generating consensus [=> ] 1.499297 s
[racon::Polisher::polish] generating consensus [==> ] 2.852647 s
[racon::Polisher::polish] generating consensus [===> ] 4.181671 s
[racon::Polisher::polish] generating consensus [====> ] 5.154441 s
[racon::Polisher::polish] generating consensus [=====> ] 5.696768 s
[racon::Polisher::polish] generating consensus [======> ] 6.181371 s
[racon::Polisher::polish] generating consensus [=======> ] 6.656474 s
[racon::Polisher::polish] generating consensus [========> ] 7.532525 s
[racon::Polisher::polish] generating consensus [=========> ] 8.594764 s
[racon::Polisher::polish] generating consensus [==========> ] 9.746290 s
[racon::Polisher::polish] generating consensus [===========> ] 11.555953 s
[racon::Polisher::polish] generating consensus [============> ] 13.837478 s
[racon::Polisher::polish] generating consensus [=============> ] 16.612178 s
[racon::Polisher::polish] generating consensus [==============> ] 19.458670 s
[racon::Polisher::polish] generating consensus [===============> ] 20.670715 s
[racon::Polisher::polish] generating consensus [================> ] 22.093187 s
[racon::Polisher::polish] generating consensus [=================> ] 23.545908 s
[racon::Polisher::polish] generating consensus [==================> ] 24.718935 s
[racon::Polisher::polish] generating consensus [===================>] 25.933817 s
[racon::Polisher::polish] generating consensus [====================] 32.033167 s
[racon::Polisher::] total = 34.789457 s
[ OK ] RaconPolishingTest.ConsensusWithQualities (34820 ms)
[ RUN ] RaconPolishingTest.ConsensusWithoutQualities
[racon::Polisher::initialize] loaded target sequences 0.003438 s
[racon::Polisher::initialize] loaded sequences 0.107572 s
[racon::Polisher::initialize] loaded overlaps 0.002100 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.142831 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.250370 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.310969 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.418910 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.528525 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.555558 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.691152 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.809551 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.900977 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 1.012358 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 1.089999 s
[racon::Polisher::initialize] aligning overlaps [============> ] 1.192463 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 1.321585 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 1.397288 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 1.514521 s
[racon::Polisher::initialize] aligning overlaps [================> ] 1.628236 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 1.719857 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 1.817419 s
[racon::Polisher::initialize] aligning overlaps [===================>] 1.945512 s
[racon::Polisher::initialize] aligning overlaps [====================] 2.091850 s
[racon::Polisher::initialize] transformed data into windows 0.003448 s
[racon::Polisher::polish] generating consensus [=> ] 1.618064 s
[racon::Polisher::polish] generating consensus [==> ] 3.452546 s
[racon::Polisher::polish] generating consensus [===> ] 4.682334 s
[racon::Polisher::polish] generating consensus [====> ] 5.713844 s
[racon::Polisher::polish] generating consensus [=====> ] 6.255580 s
[racon::Polisher::polish] generating consensus [======> ] 7.061250 s
[racon::Polisher::polish] generating consensus [=======> ] 7.680944 s
[racon::Polisher::polish] generating consensus [========> ] 8.856771 s
[racon::Polisher::polish] generating consensus [=========> ] 9.984313 s
[racon::Polisher::polish] generating consensus [==========> ] 11.718860 s
[racon::Polisher::polish] generating consensus [===========> ] 13.570560 s
[racon::Polisher::polish] generating consensus [============> ] 15.767746 s
[racon::Polisher::polish] generating consensus [=============> ] 18.995381 s
[racon::Polisher::polish] generating consensus [==============> ] 21.362593 s
[racon::Polisher::polish] generating consensus [===============> ] 23.734539 s
[racon::Polisher::polish] generating consensus [================> ] 25.663137 s
[racon::Polisher::polish] generating consensus [=================> ] 28.009008 s
[racon::Polisher::polish] generating consensus [==================> ] 29.327399 s
[racon::Polisher::polish] generating consensus [===================>] 30.862834 s
[racon::Polisher::polish] generating consensus [====================] 39.915509 s
[racon::Polisher::] total = 42.223231 s
[ OK ] RaconPolishingTest.ConsensusWithoutQualities (42251 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments
[racon::Polisher::initialize] loaded target sequences 0.003461 s
[racon::Polisher::initialize] loaded sequences 0.232342 s
[racon::Polisher::initialize] loaded overlaps 0.140765 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.044522 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.044813 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.045062 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.045304 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.045545 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.059561 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.059631 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.059687 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.059738 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.059789 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.059840 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.064568 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.064633 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.064687 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.064736 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.064785 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.064835 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.068265 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.068330 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.068384 s
[racon::Polisher::initialize] transformed data into windows 0.017394 s
[racon::Polisher::polish] generating consensus [=> ] 1.628009 s
[racon::Polisher::polish] generating consensus [==> ] 3.086915 s
[racon::Polisher::polish] generating consensus [===> ] 4.001640 s
[racon::Polisher::polish] generating consensus [====> ] 4.850127 s
[racon::Polisher::polish] generating consensus [=====> ] 4.998926 s
[racon::Polisher::polish] generating consensus [======> ] 5.466354 s
[racon::Polisher::polish] generating consensus [=======> ] 5.971989 s
[racon::Polisher::polish] generating consensus [========> ] 6.738024 s
[racon::Polisher::polish] generating consensus [=========> ] 7.526452 s
[racon::Polisher::polish] generating consensus [==========> ] 8.538364 s
[racon::Polisher::polish] generating consensus [===========> ] 10.002141 s
[racon::Polisher::polish] generating consensus [============> ] 11.386210 s
[racon::Polisher::polish] generating consensus [=============> ] 13.784194 s
[racon::Polisher::polish] generating consensus [==============> ] 16.312367 s
[racon::Polisher::polish] generating consensus [===============> ] 17.877046 s
[racon::Polisher::polish] generating consensus [================> ] 19.300855 s
[racon::Polisher::polish] generating consensus [=================> ] 20.743555 s
[racon::Polisher::polish] generating consensus [==================> ] 21.815158 s
[racon::Polisher::polish] generating consensus [===================>] 22.853796 s
[racon::Polisher::polish] generating consensus [====================] 28.646099 s
[racon::Polisher::] total = 29.214692 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments (29242 ms)
[ RUN ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments
[racon::Polisher::initialize] loaded target sequences 0.003330 s
[racon::Polisher::initialize] loaded sequences 0.107417 s
[racon::Polisher::initialize] loaded overlaps 0.140440 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.016843 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.018336 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.019874 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.021694 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.022907 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.024169 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.026085 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.037491 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.037736 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 0.037975 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 0.038210 s
[racon::Polisher::initialize] aligning overlaps [============> ] 0.038448 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 0.038685 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 0.047296 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 0.047729 s
[racon::Polisher::initialize] aligning overlaps [================> ] 0.047968 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 0.048209 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 0.048452 s
[racon::Polisher::initialize] aligning overlaps [===================>] 0.048690 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.048927 s
[racon::Polisher::initialize] transformed data into windows 0.003334 s
[racon::Polisher::polish] generating consensus [=> ] 1.392686 s
[racon::Polisher::polish] generating consensus [==> ] 2.908305 s
[racon::Polisher::polish] generating consensus [===> ] 4.176409 s
[racon::Polisher::polish] generating consensus [====> ] 5.033180 s
[racon::Polisher::polish] generating consensus [=====> ] 5.678246 s
[racon::Polisher::polish] generating consensus [======> ] 6.348521 s
[racon::Polisher::polish] generating consensus [=======> ] 7.005033 s
[racon::Polisher::polish] generating consensus [========> ] 8.207507 s
[racon::Polisher::polish] generating consensus [=========> ] 8.959075 s
[racon::Polisher::polish] generating consensus [==========> ] 10.608948 s
[racon::Polisher::polish] generating consensus [===========> ] 12.255031 s
[racon::Polisher::polish] generating consensus [============> ] 14.233513 s
[racon::Polisher::polish] generating consensus [=============> ] 17.384087 s
[racon::Polisher::polish] generating consensus [==============> ] 19.852444 s
[racon::Polisher::polish] generating consensus [===============> ] 22.021331 s
[racon::Polisher::polish] generating consensus [================> ] 24.074771 s
[racon::Polisher::polish] generating consensus [=================> ] 26.292108 s
[racon::Polisher::polish] generating consensus [==================> ] 27.557086 s
[racon::Polisher::polish] generating consensus [===================>] 28.835002 s
[racon::Polisher::polish] generating consensus [====================] 36.892471 s
[racon::Polisher::] total = 37.273325 s
[ OK ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments (37305 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow
[racon::Polisher::initialize] loaded target sequences 0.003366 s
[racon::Polisher::initialize] loaded sequences 0.232914 s
[racon::Polisher::initialize] loaded overlaps 0.002062 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.137604 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.235391 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.300386 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.419218 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.533899 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.564914 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.702071 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.822850 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.906932 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 1.014758 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 1.093508 s
[racon::Polisher::initialize] aligning overlaps [============> ] 1.199543 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 1.335584 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 1.413579 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 1.531005 s
[racon::Polisher::initialize] aligning overlaps [================> ] 1.646431 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 1.734794 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 1.854132 s
[racon::Polisher::initialize] aligning overlaps [===================>] 2.033128 s
[racon::Polisher::initialize] aligning overlaps [====================] 2.127813 s
[racon::Polisher::initialize] transformed data into windows 0.016413 s
[racon::Polisher::polish] generating consensus [=> ] 4.958129 s
[racon::Polisher::polish] generating consensus [==> ] 4.958296 s
[racon::Polisher::polish] generating consensus [===> ] 9.581775 s
[racon::Polisher::polish] generating consensus [====> ] 9.582174 s
[racon::Polisher::polish] generating consensus [=====> ] 10.149691 s
[racon::Polisher::polish] generating consensus [======> ] 11.303129 s
[racon::Polisher::polish] generating consensus [=======> ] 11.878089 s
[racon::Polisher::polish] generating consensus [========> ] 13.775978 s
[racon::Polisher::polish] generating consensus [=========> ] 15.356424 s
[racon::Polisher::polish] generating consensus [==========> ] 17.858748 s
[racon::Polisher::polish] generating consensus [===========> ] 21.765267 s
[racon::Polisher::polish] generating consensus [============> ] 24.018337 s
[racon::Polisher::polish] generating consensus [=============> ] 31.628713 s
[racon::Polisher::polish] generating consensus [==============> ] 33.087146 s
[racon::Polisher::polish] generating consensus [===============> ] 38.284570 s
[racon::Polisher::polish] generating consensus [================> ] 38.284854 s
[racon::Polisher::polish] generating consensus [=================> ] 42.824531 s
[racon::Polisher::polish] generating consensus [==================> ] 42.824687 s
[racon::Polisher::polish] generating consensus [===================>] 46.839936 s
[racon::Polisher::polish] generating consensus [====================] 57.311154 s
[racon::Polisher::] total = 59.810265 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow (59854 ms)
[ RUN ] RaconPolishingTest.ConsensusWithQualitiesEditDistance
[racon::Polisher::initialize] loaded target sequences 0.003457 s
[racon::Polisher::initialize] loaded sequences 0.231788 s
[racon::Polisher::initialize] loaded overlaps 0.002037 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.147873 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.252891 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.319822 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.430772 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.580245 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.589507 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.727354 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.849658 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.919199 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 1.047331 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 1.125554 s
[racon::Polisher::initialize] aligning overlaps [============> ] 1.229282 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 1.366750 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 1.434982 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 1.552320 s
[racon::Polisher::initialize] aligning overlaps [================> ] 1.674875 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 1.792527 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 1.873973 s
[racon::Polisher::initialize] aligning overlaps [===================>] 2.028750 s
[racon::Polisher::initialize] aligning overlaps [====================] 2.168373 s
[racon::Polisher::initialize] transformed data into windows 0.017506 s
[racon::Polisher::polish] generating consensus [=> ] 1.307128 s
[racon::Polisher::polish] generating consensus [==> ] 2.521283 s
[racon::Polisher::polish] generating consensus [===> ] 3.801976 s
[racon::Polisher::polish] generating consensus [====> ] 4.535915 s
[racon::Polisher::polish] generating consensus [=====> ] 4.797812 s
[racon::Polisher::polish] generating consensus [======> ] 5.244444 s
[racon::Polisher::polish] generating consensus [=======> ] 5.671704 s
[racon::Polisher::polish] generating consensus [========> ] 6.385011 s
[racon::Polisher::polish] generating consensus [=========> ] 7.220462 s
[racon::Polisher::polish] generating consensus [==========> ] 8.218633 s
[racon::Polisher::polish] generating consensus [===========> ] 9.684728 s
[racon::Polisher::polish] generating consensus [============> ] 11.545335 s
[racon::Polisher::polish] generating consensus [=============> ] 13.713767 s
[racon::Polisher::polish] generating consensus [==============> ] 16.141122 s
[racon::Polisher::polish] generating consensus [===============> ] 17.352438 s
[racon::Polisher::polish] generating consensus [================> ] 18.928743 s
[racon::Polisher::polish] generating consensus [=================> ] 20.468594 s
[racon::Polisher::polish] generating consensus [==================> ] 21.333521 s
[racon::Polisher::polish] generating consensus [===================>] 22.487873 s
[racon::Polisher::polish] generating consensus [====================] 28.165787 s
[racon::Polisher::] total = 30.689182 s
[ OK ] RaconPolishingTest.ConsensusWithQualitiesEditDistance (30718 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualities
[racon::Polisher::initialize] loaded target sequences 0.233310 s
[racon::Polisher::initialize] loaded sequences 0.239672 s
[racon::Polisher::initialize] loaded overlaps 0.064632 s
[racon::Polisher::initialize] aligning overlaps [=> ] 0.171501 s
[racon::Polisher::initialize] aligning overlaps [==> ] 0.267760 s
[racon::Polisher::initialize] aligning overlaps [===> ] 0.375808 s
[racon::Polisher::initialize] aligning overlaps [====> ] 0.447018 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 0.537254 s
[racon::Polisher::initialize] aligning overlaps [======> ] 0.593587 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 0.700155 s
[racon::Polisher::initialize] aligning overlaps [========> ] 0.775303 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 0.921428 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 1.013291 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 1.082960 s
[racon::Polisher::initialize] aligning overlaps [============> ] 1.212832 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 1.353418 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 1.475135 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 1.600672 s
[racon::Polisher::initialize] aligning overlaps [================> ] 1.731214 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 1.828516 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 2.031906 s
[racon::Polisher::initialize] aligning overlaps [===================>] 2.096592 s
[racon::Polisher::initialize] aligning overlaps [====================] 2.413732 s
[racon::Polisher::initialize] transformed data into windows 0.029346 s
[racon::Polisher::polish] generating consensus [=> ] 0.881620 s
[racon::Polisher::polish] generating consensus [==> ] 1.845016 s
[racon::Polisher::polish] generating consensus [===> ] 2.775986 s
[racon::Polisher::polish] generating consensus [====> ] 2.776895 s
[racon::Polisher::polish] generating consensus [=====> ] 3.392136 s
[racon::Polisher::polish] generating consensus [======> ] 3.845557 s
[racon::Polisher::polish] generating consensus [=======> ] 4.442279 s
[racon::Polisher::polish] generating consensus [========> ] 4.493161 s
[racon::Polisher::polish] generating consensus [=========> ] 5.822219 s
[racon::Polisher::polish] generating consensus [==========> ] 6.303203 s
[racon::Polisher::polish] generating consensus [===========> ] 6.744843 s
[racon::Polisher::polish] generating consensus [============> ] 6.989465 s
[racon::Polisher::polish] generating consensus [=============> ] 7.483837 s
[racon::Polisher::polish] generating consensus [==============> ] 7.484700 s
[racon::Polisher::polish] generating consensus [===============> ] 8.797966 s
[racon::Polisher::polish] generating consensus [================> ] 8.798865 s
[racon::Polisher::polish] generating consensus [=================> ] 11.213243 s
[racon::Polisher::polish] generating consensus [==================> ] 12.021997 s
[racon::Polisher::polish] generating consensus [===================>] 13.019038 s
[racon::Polisher::polish] generating consensus [====================] 13.495045 s
[racon::Polisher::] total = 16.481766 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualities (16509 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull
[racon::Polisher::initialize] loaded target sequences 0.232635 s
[racon::Polisher::initialize] loaded sequences 0.236134 s
[racon::Polisher::initialize] loaded overlaps 0.062814 s
[racon::Polisher::initialize] aligning overlaps [=> ] 2.621698 s
[racon::Polisher::initialize] aligning overlaps [==> ] 4.415227 s
[racon::Polisher::initialize] aligning overlaps [===> ] 6.087125 s
[racon::Polisher::initialize] aligning overlaps [====> ] 8.353965 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 10.165996 s
[racon::Polisher::initialize] aligning overlaps [======> ] 11.724860 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 13.720841 s
[racon::Polisher::initialize] aligning overlaps [========> ] 16.221538 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 18.778913 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 21.050758 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 22.945385 s
[racon::Polisher::initialize] aligning overlaps [============> ] 25.569599 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 28.295582 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 30.637357 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 33.445520 s
[racon::Polisher::initialize] aligning overlaps [================> ] 36.161780 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 38.646558 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 41.314093 s
[racon::Polisher::initialize] aligning overlaps [===================>] 44.168741 s
[racon::Polisher::initialize] aligning overlaps [====================] 47.784751 s
[racon::Polisher::initialize] transformed data into windows 0.492057 s
[racon::Polisher::polish] generating consensus [=> ] 50.730889 s
[racon::Polisher::polish] generating consensus [==> ] 83.026080 s
[racon::Polisher::polish] generating consensus [===> ] 120.440829 s
[racon::Polisher::polish] generating consensus [====> ] 150.717624 s
[racon::Polisher::polish] generating consensus [=====> ] 186.133490 s
[racon::Polisher::polish] generating consensus [======> ] 226.014401 s
[racon::Polisher::polish] generating consensus [=======> ] 265.462599 s
[racon::Polisher::polish] generating consensus [========> ] 295.653209 s
[racon::Polisher::polish] generating consensus [=========> ] 336.296302 s
[racon::Polisher::polish] generating consensus [==========> ] 380.742090 s
[racon::Polisher::polish] generating consensus [===========> ] 417.842189 s
[racon::Polisher::polish] generating consensus [============> ] 459.739290 s
[racon::Polisher::polish] generating consensus [=============> ] 497.122072 s
[racon::Polisher::polish] generating consensus [==============> ] 537.162962 s
[racon::Polisher::polish] generating consensus [===============> ] 578.774040 s
[racon::Polisher::polish] generating consensus [================> ] 603.605931 s
[racon::Polisher::polish] generating consensus [=================> ] 652.018703 s
[racon::Polisher::polish] generating consensus [==================> ] 693.240904 s
[racon::Polisher::polish] generating consensus [===================>] 734.557609 s
[racon::Polisher::polish] generating consensus [====================] 773.061673 s
[racon::Polisher::] total = 821.894354 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull (821923 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull
[racon::Polisher::initialize] loaded target sequences 0.107472 s
[racon::Polisher::initialize] loaded sequences 0.107890 s
[racon::Polisher::initialize] loaded overlaps 0.062770 s
[racon::Polisher::initialize] aligning overlaps [=> ] 2.574372 s
[racon::Polisher::initialize] aligning overlaps [==> ] 4.891943 s
[racon::Polisher::initialize] aligning overlaps [===> ] 6.545010 s
[racon::Polisher::initialize] aligning overlaps [====> ] 8.824022 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 10.629327 s
[racon::Polisher::initialize] aligning overlaps [======> ] 12.187199 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 14.160575 s
[racon::Polisher::initialize] aligning overlaps [========> ] 16.637722 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 19.160838 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 21.424048 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 23.256767 s
[racon::Polisher::initialize] aligning overlaps [============> ] 25.847789 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 28.540086 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 30.880921 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 33.660007 s
[racon::Polisher::initialize] aligning overlaps [================> ] 36.374470 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 38.882367 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 41.522338 s
[racon::Polisher::initialize] aligning overlaps [===================>] 44.295993 s
[racon::Polisher::initialize] aligning overlaps [====================] 46.878524 s
[racon::Polisher::initialize] transformed data into windows 0.114699 s
[racon::Polisher::polish] generating consensus [=> ] 65.087339 s
[racon::Polisher::polish] generating consensus [==> ] 117.604414 s
[racon::Polisher::polish] generating consensus [===> ] 168.691759 s
[racon::Polisher::polish] generating consensus [====> ] 208.120759 s
[racon::Polisher::polish] generating consensus [=====> ] 256.491138 s
[racon::Polisher::polish] generating consensus [======> ] 309.680090 s
[racon::Polisher::polish] generating consensus [=======> ] 365.170533 s
[racon::Polisher::polish] generating consensus [========> ] 411.845835 s
[racon::Polisher::polish] generating consensus [=========> ] 463.414487 s
[racon::Polisher::polish] generating consensus [==========> ] 525.302955 s
[racon::Polisher::polish] generating consensus [===========> ] 578.336397 s
[racon::Polisher::polish] generating consensus [============> ] 634.775426 s
[racon::Polisher::polish] generating consensus [=============> ] 690.044548 s
[racon::Polisher::polish] generating consensus [==============> ] 746.326485 s
[racon::Polisher::polish] generating consensus [===============> ] 800.874427 s
[racon::Polisher::polish] generating consensus [================> ] 831.287093 s
[racon::Polisher::polish] generating consensus [=================> ] 898.603311 s
[racon::Polisher::polish] generating consensus [==================> ] 961.160738 s
[racon::Polisher::polish] generating consensus [===================>] 1024.618659 s
[racon::Polisher::polish] generating consensus [====================] 1078.146134 s
[racon::Polisher::] total = 1125.441064 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull (1125471 ms)
[ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap
[racon::Polisher::initialize] loaded target sequences 0.233090 s
[racon::Polisher::initialize] loaded sequences 0.233962 s
[racon::Polisher::initialize] loaded overlaps 0.067820 s
[racon::Polisher::initialize] aligning overlaps [=> ] 2.576486 s
[racon::Polisher::initialize] aligning overlaps [==> ] 4.394659 s
[racon::Polisher::initialize] aligning overlaps [===> ] 6.034790 s
[racon::Polisher::initialize] aligning overlaps [====> ] 8.329879 s
[racon::Polisher::initialize] aligning overlaps [=====> ] 10.104186 s
[racon::Polisher::initialize] aligning overlaps [======> ] 11.655214 s
[racon::Polisher::initialize] aligning overlaps [=======> ] 13.641980 s
[racon::Polisher::initialize] aligning overlaps [========> ] 16.092882 s
[racon::Polisher::initialize] aligning overlaps [=========> ] 18.612949 s
[racon::Polisher::initialize] aligning overlaps [==========> ] 20.894946 s
[racon::Polisher::initialize] aligning overlaps [===========> ] 22.740913 s
[racon::Polisher::initialize] aligning overlaps [============> ] 25.350677 s
[racon::Polisher::initialize] aligning overlaps [=============> ] 28.060766 s
[racon::Polisher::initialize] aligning overlaps [==============> ] 30.417130 s
[racon::Polisher::initialize] aligning overlaps [===============> ] 33.197464 s
[racon::Polisher::initialize] aligning overlaps [================> ] 35.935215 s
[racon::Polisher::initialize] aligning overlaps [=================> ] 38.417937 s
[racon::Polisher::initialize] aligning overlaps [==================> ] 41.074877 s
[racon::Polisher::initialize] aligning overlaps [===================>] 43.846823 s
[racon::Polisher::initialize] aligning overlaps [====================] 46.439555 s
[racon::Polisher::initialize] transformed data into windows 0.506181 s
[racon::Polisher::polish] generating consensus [=> ] 47.499812 s
[racon::Polisher::polish] generating consensus [==> ] 79.748645 s
[racon::Polisher::polish] generating consensus [===> ] 117.426029 s
[racon::Polisher::polish] generating consensus [====> ] 147.555740 s
[racon::Polisher::polish] generating consensus [=====> ] 186.277822 s
[racon::Polisher::polish] generating consensus [======> ] 226.137273 s
[racon::Polisher::polish] generating consensus [=======> ] 265.785971 s
[racon::Polisher::polish] generating consensus [========> ] 295.771733 s
[racon::Polisher::polish] generating consensus [=========> ] 333.160777 s
[racon::Polisher::polish] generating consensus [==========> ] 377.708476 s
[racon::Polisher::polish] generating consensus [===========> ] 414.730314 s
[racon::Polisher::polish] generating consensus [============> ] 457.154438 s
[racon::Polisher::polish] generating consensus [=============> ] 496.494584 s
[racon::Polisher::polish] generating consensus [==============> ] 536.795253 s
[racon::Polisher::polish] generating consensus [===============> ] 578.486917 s
[racon::Polisher::polish] generating consensus [================> ] 602.507396 s
[racon::Polisher::polish] generating consensus [=================> ] 648.354828 s
[racon::Polisher::polish] generating consensus [==================> ] 689.599697 s
[racon::Polisher::polish] generating consensus [===================>] 730.828054 s
[racon::Polisher::polish] generating consensus [====================] 773.853918 s
[racon::Polisher::] total = 821.359497 s
[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap (821388 ms)
[----------] 10 tests from RaconPolishingTest (3019484 ms total)
[----------] Global test environment tear-down
[==========] 15 tests from 2 test suites ran. (3019556 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 -a -O--buildsystem=cmake
cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/racon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<PKGBUILDDIR>>/debian/racon/usr/bin/racon
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
dh_install -a -O--buildsystem=cmake
dh_installdocs -a -O--buildsystem=cmake
dh_installchangelogs -a -O--buildsystem=cmake
dh_installexamples -a -O--buildsystem=cmake
dh_installman -a -O--buildsystem=cmake
dh_installsystemduser -a -O--buildsystem=cmake
dh_lintian -a -O--buildsystem=cmake
dh_perl -a -O--buildsystem=cmake
dh_link -a -O--buildsystem=cmake
dh_strip_nondeterminism -a -O--buildsystem=cmake
dh_compress -a -O--buildsystem=cmake
dh_fixperms -a -O--buildsystem=cmake
dh_missing -a -O--buildsystem=cmake
dh_dwz -a -a -O--buildsystem=cmake
dh_strip -a -a -O--buildsystem=cmake
dh_makeshlibs -a -a -O--buildsystem=cmake
dh_shlibdeps -a -a -O--buildsystem=cmake
dpkg-shlibdeps: warning: debian/racon/usr/bin/racon contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/racon/usr/lib/racon/racon_test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/racon/usr/bin/racon debian/racon/usr/lib/racon/racon_test were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a -O--buildsystem=cmake
dh_gencontrol -a -O--buildsystem=cmake
dh_md5sums -a -O--buildsystem=cmake
dh_builddeb -a -O--buildsystem=cmake
dpkg-deb: building package 'racon-dbgsym' in '../racon-dbgsym_1.4.20-1_armhf.deb'.
dpkg-deb: building package 'racon' in '../racon_1.4.20-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../racon_1.4.20-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-01-20T01:06:26Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
racon_1.4.20-1_armhf.changes:
-----------------------------
Format: 1.8
Date: Tue, 19 Jan 2021 08:11:15 +0100
Source: racon
Binary: racon racon-dbgsym
Architecture: armhf
Version: 1.4.20-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <crusoe@debian.org>
Description:
racon - consensus module for raw de novo DNA assembly of long uncorrected
Changes:
racon (1.4.20-1) unstable; urgency=medium
.
* Team upload.
.
[ Andreas Tille ]
* Add lintian-override
* Standards-Version: 4.5.1 (routine-update)
.
[ Michael R. Crusoe ]
* Update patches.
* Build the wrapper script.
* Bump libthread-pool-dev build-dep to be at least 3
* libthread-pool-dev is now header-only, update use_debian_packaged_libs.patch
to reflect that.
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Checksums-Sha256:
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Files:
09cfb66af5c3e4398b3ca44fa63967cd 3219508 debug optional racon-dbgsym_1.4.20-1_armhf.deb
4e99fb60983a230be9f538e581369ffb 5978 science optional racon_1.4.20-1_armhf.buildinfo
cf135e55f9e3cf26b8e00d31669ddfe4 3235656 science optional racon_1.4.20-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
racon-dbgsym_1.4.20-1_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 3219508 bytes: control archive=640 bytes.
406 bytes, 12 lines control
297 bytes, 3 lines md5sums
Package: racon-dbgsym
Source: racon
Version: 1.4.20-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3439
Depends: racon (= 1.4.20-1)
Section: debug
Priority: optional
Description: debug symbols for racon
Build-Ids: 48edab9227c06cda33187ae0a258bdf365772c14 524d08b2c0172cdb590a4ea042a64edacb8f83a0
drwxr-xr-x root/root 0 2021-01-19 07:11 ./
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/lib/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/lib/debug/.build-id/48/
-rw-r--r-- root/root 2403272 2021-01-19 07:11 ./usr/lib/debug/.build-id/48/edab9227c06cda33187ae0a258bdf365772c14.debug
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/lib/debug/.build-id/52/
-rw-r--r-- root/root 781336 2021-01-19 07:11 ./usr/lib/debug/.build-id/52/4d08b2c0172cdb590a4ea042a64edacb8f83a0.debug
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 321732 2021-01-19 07:11 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/racon.debug
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/share/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-01-19 07:11 ./usr/share/doc/racon-dbgsym -> racon
racon_1.4.20-1_armhf.deb
------------------------
new Debian package, version 2.0.
size 3235656 bytes: control archive=1824 bytes.
2117 bytes, 41 lines control
1174 bytes, 15 lines md5sums
Package: racon
Version: 1.4.20-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3694
Depends: libc6 (>= 2.28), libedlib0 (>= 1.2.3), libgcc-s1 (>= 3.5), libspoa7.0.0 (>= 4.0.6+ds2), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4)
Recommends: python3, rampler
Section: science
Priority: optional
Homepage: https://github.com/lbcb-sci/racon
Description: consensus module for raw de novo DNA assembly of long uncorrected reads
Racon is intended as a standalone consensus module to correct raw
contigs generated by rapid assembly methods which do not include a
consensus step. The goal of Racon is to generate genomic consensus which
is of similar or better quality compared to the output generated by
assembly methods which employ both error correction and consensus steps,
while providing a speedup of several times compared to those methods. It
supports data produced by both Pacific Biosciences and Oxford Nanopore
Technologies.
.
Racon can be used as a polishing tool after the assembly with either
Illumina data or data produced by third generation of sequencing. The
type of data inputed is automatically detected.
.
Racon takes as input only three files: contigs in FASTA/FASTQ format,
reads in FASTA/FASTQ format and overlaps/alignments between the reads
and the contigs in MHAP/PAF/SAM format. Output is a set of polished
contigs in FASTA format printed to stdout. All input files can be
compressed with gzip.
.
Racon can also be used as a read error-correction tool. In this
scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps
between reads including dual overlaps.
.
A wrapper script is also available to enable easier usage to the end-
user for large datasets. It has the same interface as racon but adds
two additional features from the outside. Sequences can be subsampled
to decrease the total execution time (accuracy might be lower) while
target sequences can be split into smaller chunks and run sequentially
to decrease memory consumption. Both features can be run at the same
time as well.
drwxr-xr-x root/root 0 2021-01-19 07:11 ./
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/bin/
-rwxr-xr-x root/root 149340 2021-01-19 07:11 ./usr/bin/racon
-rwxr-xr-x root/root 9854 2021-01-19 07:11 ./usr/bin/racon_wrapper.py
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/lib/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/lib/racon/
-rwxr-xr-x root/root 550540 2021-01-19 07:11 ./usr/lib/racon/racon_test
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/share/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/share/doc/racon/
-rw-r--r-- root/root 838 2021-01-19 07:11 ./usr/share/doc/racon/changelog.Debian.gz
-rw-r--r-- root/root 1481 2021-01-19 07:11 ./usr/share/doc/racon/copyright
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/share/doc/racon/examples/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/share/doc/racon/examples/data/
-rw-r--r-- root/root 146882 2021-01-19 07:11 ./usr/share/doc/racon/examples/data/sample_ava_overlaps.mhap.gz
-rw-r--r-- root/root 151632 2021-01-19 07:11 ./usr/share/doc/racon/examples/data/sample_ava_overlaps.paf.gz
-rw-r--r-- root/root 14197 2021-01-19 07:11 ./usr/share/doc/racon/examples/data/sample_layout.fasta.gz
-rw-r--r-- root/root 5111 2021-01-19 07:11 ./usr/share/doc/racon/examples/data/sample_overlaps.paf.gz
-rw-r--r-- root/root 698977 2021-01-19 07:11 ./usr/share/doc/racon/examples/data/sample_overlaps.sam.gz
-rw-r--r-- root/root 488701 2021-01-19 07:11 ./usr/share/doc/racon/examples/data/sample_reads.fasta.gz
-rw-r--r-- root/root 1526281 2021-01-19 07:11 ./usr/share/doc/racon/examples/data/sample_reads.fastq.gz
-rw-r--r-- root/root 15195 2021-01-19 07:11 ./usr/share/doc/racon/examples/data/sample_reference.fasta.gz
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/share/lintian/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 114 2021-01-18 15:54 ./usr/share/lintian/overrides/racon
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/share/man/
drwxr-xr-x root/root 0 2021-01-19 07:11 ./usr/share/man/man1/
-rw-r--r-- root/root 1472 2021-01-19 07:11 ./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: 44836
Build-Time: 3200
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 422
Job: racon_1.4.20-1
Machine Architecture: armhf
Package: racon
Package-Time: 3672
Source-Version: 1.4.20-1
Space: 44836
Status: successful
Version: 1.4.20-1
--------------------------------------------------------------------------------
Finished at 2021-01-20T01:06:26Z
Build needed 01:01:12, 44836k disc space