tvc →
5.0.3+git20151221.80e144e+dfsg-4+b1 →
armhf → 2021-12-15 23:19:02
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+=================================================================================+
| tvc 5.0.3+git20151221.80e144e+dfsg-4+b1 (armhf) Wed, 15 Dec 2021 23:05:47 +0000 |
+=================================================================================+
Package: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-4+b1
Source Version: 5.0.3+git20151221.80e144e+dfsg-4
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-19c77207-3dfd-4e3b-b5b3-a7bf93c072aa' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [12.6 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.5 MB]
Fetched 26.2 MB in 11s (2455 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: 'tvc' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/tvc.git
Please use:
git clone https://salsa.debian.org/med-team/tvc.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 756 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-4 (dsc) [2200 B]
Get:2 http://172.17.4.1/private bookworm-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-4 (tar) [745 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-4 (diff) [9248 B]
Fetched 756 kB in 0s (2845 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/tvc-TLu8QM/tvc-5.0.3+git20151221.80e144e+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/tvc-TLu8QM' 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-uJYHFP/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-uJYHFP/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-uJYHFP/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-uJYHFP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uJYHFP/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uJYHFP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uJYHFP/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uJYHFP/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (10.3 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 33 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-uJYHFP/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (68.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12559 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev
Filtered Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev
dpkg-deb: building package 'sbuild-build-depends-tvc-dummy' in '/<<BUILDDIR>>/resolver-uJYHFP/apt_archive/sbuild-build-depends-tvc-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-tvc-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-uJYHFP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uJYHFP/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uJYHFP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uJYHFP/apt_archive ./ Sources [535 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uJYHFP/apt_archive ./ Packages [617 B]
Fetched 2485 B in 0s (11.3 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install tvc build dependencies (apt-based resolver)
---------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
cpp-11 debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file g++-11 gcc-10-base gcc-11 gcc-11-base gettext
gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarchive13 libarmadillo-dev libarmadillo10 libarpack2
libarpack2-dev libasan6 libatomic1 libbamtools-dev libbamtools2.5.1
libblas-dev libblas3 libboost-math-dev libboost-math1.74-dev
libboost-math1.74.0 libboost1.74-dev libbrotli1 libcc1-0 libcurl4
libcurl4-openssl-dev libdebhelper-perl libdisorder-dev libdisorder0 libelf1
libexpat1 libfile-stripnondeterminism-perl libgcc-10-dev libgcc-11-dev
libgcc-s1 libgfortran5 libgomp1 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev
libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100
libicu67 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev
libjsoncpp25 liblapack-dev liblapack3 libmagic-mgc libmagic1 libncurses6
libnghttp2-14 libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2
libsmithwaterman-dev libsmithwaterman0 libssh2-1 libssl-dev libstdc++-10-dev
libstdc++-11-dev libstdc++6 libsub-override-perl libsuperlu-dev libsuperlu5
libsz2 libtool libubsan1 libuchardet0 libuv1 libxml2 m4 man-db po-debconf
procps zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build
cmake-format gcc-11-locales dh-make gcc-11-doc gettext-doc libasprintf-dev
libgettextpo-dev groff lrzip libitpp-dev libbamtools-doc liblapack-doc
libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev
libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-mpi1.74-dev
libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-program-options1.74-dev libboost-python1.74-dev
libboost-random1.74-dev libboost-regex1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev
pkg-config libhdf5-doc libssl-doc libstdc++-10-doc libstdc++-11-doc
libsuperlu-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libgpm2 publicsuffix
libltdl-dev libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file gcc-10-base gettext gettext-base groff-base hdf5-helpers
intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13
libarmadillo-dev libarmadillo10 libarpack2 libarpack2-dev libbamtools-dev
libbamtools2.5.1 libblas-dev libblas3 libboost-math-dev
libboost-math1.74-dev libboost-math1.74.0 libboost1.74-dev libbrotli1
libcurl4 libcurl4-openssl-dev libdebhelper-perl libdisorder-dev libdisorder0
libelf1 libexpat1 libfile-stripnondeterminism-perl libgcc-10-dev
libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu67
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev libjsoncpp25
liblapack-dev liblapack3 libmagic-mgc libmagic1 libncurses6 libnghttp2-14
libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2
libsmithwaterman-dev libsmithwaterman0 libssh2-1 libssl-dev libstdc++-10-dev
libsub-override-perl libsuperlu-dev libsuperlu5 libsz2 libtool libuchardet0
libuv1 libxml2 m4 man-db po-debconf procps sbuild-build-depends-tvc-dummy
zlib1g-dev
The following packages will be upgraded:
cpp-11 g++-11 gcc-11 gcc-11-base libasan6 libatomic1 libcc1-0 libgcc-11-dev
libgcc-s1 libgomp1 libstdc++-11-dev libstdc++6 libubsan1
13 upgraded, 91 newly installed, 0 to remove and 20 not upgraded.
Need to get 86.1 MB of archives.
After this operation, 5802 kB disk space will be freed.
Get:1 copy:/<<BUILDDIR>>/resolver-uJYHFP/apt_archive ./ sbuild-build-depends-tvc-dummy 0.invalid.0 [908 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libcc1-0 armhf 11.2.0-12+rpi1 [37.9 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf gcc-11-base armhf 11.2.0-12+rpi1 [206 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libgcc-s1 armhf 11.2.0-12+rpi1 [36.3 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libgomp1 armhf 11.2.0-12+rpi1 [88.1 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libatomic1 armhf 11.2.0-12+rpi1 [8184 B]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libasan6 armhf 11.2.0-12+rpi1 [1947 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libubsan1 armhf 11.2.0-12+rpi1 [798 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf g++-11 armhf 11.2.0-12+rpi1 [7905 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-11-dev armhf 11.2.0-12+rpi1 [1957 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libgcc-11-dev armhf 11.2.0-12+rpi1 [698 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf gcc-11 armhf 11.2.0-12+rpi1 [14.0 MB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf cpp-11 armhf 11.2.0-12+rpi1 [7070 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libstdc++6 armhf 11.2.0-12+rpi1 [466 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-1 [31.6 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf gcc-10-base armhf 10.3.0-13+rpi1 [206 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3-1 [79.8 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-5 [60.5 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-5 [475 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.79.1-2 [320 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-3 [80.1 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp25 armhf 1.9.5-2 [67.0 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf librhash0 armhf 1.4.2-1 [141 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libuv1 armhf 1.42.0-1 [121 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf dh-elpa-helper all 2.0.9 [11.2 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf emacsen-common all 3.0.4 [19.3 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf cmake-data all 3.22.1-1 [1905 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf cmake armhf 3.22.1-1+b1 [3478 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.1-1 [26.5 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.1-1 [15.6 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf hdf5-helpers armhf 1.10.7+repack-4+rpi1 [42.9 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libaec0 armhf 1.0.6-1 [19.3 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libsz2 armhf 1.0.6-1 [7452 B]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libaec-dev armhf 1.0.6-1 [17.6 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.0-1 [108 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-12+rpi1 [235 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.0-1 [1594 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libarpack2 armhf 3.8.0-1 [85.9 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libsuperlu5 armhf 5.3.0+dfsg1-2 [128 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libarmadillo10 armhf 1:10.7.4+dfsg-1 [99.0 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.0-1 [113 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.0-1 [2872 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libarpack2-dev armhf 3.8.0-1 [94.6 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-103-1 armhf 1.10.7+repack-4+rpi1 [1246 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-fortran-102 armhf 1.10.7+repack-4+rpi1 [97.0 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-100 armhf 1.10.7+repack-4+rpi1 [82.1 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.7+repack-4+rpi1 [53.9 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.7+repack-4+rpi1 [133 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.7+repack-4+rpi1 [40.1 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.2-1 [261 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.1.2-1 [74.7 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-openssl-dev armhf 7.79.1-2 [396 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 1.1.1l-1 [1581 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-dev armhf 1.10.7+repack-4+rpi1 [2211 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libsuperlu-dev armhf 5.3.0+dfsg1-2 [22.1 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libarmadillo-dev armhf 1:10.7.4+dfsg-1 [401 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-10 [134 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-10 [178 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libgcc-10-dev armhf 10.3.0-13+rpi1 [679 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-10-dev armhf 10.3.0-13+rpi1 [1758 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-13 [9537 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libboost-math1.74.0 armhf 1.74.0-13 [344 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libboost-math1.74-dev armhf 1.74.0-13 [402 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libboost-math-dev armhf 1.74.0.3+b2 [4804 B]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-4 [4856 B]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-4 [4484 B]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp-dev armhf 1.9.5-2 [26.3 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12 [32.4 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-12 [36.7 kB]
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Preparing to unpack .../85-libdisorder-dev_0.0.2+git20130809.8062ee1-4_armhf.deb ...
Unpacking libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-4) ...
Selecting previously unselected package libjsoncpp-dev:armhf.
Preparing to unpack .../86-libjsoncpp-dev_1.9.5-2_armhf.deb ...
Unpacking libjsoncpp-dev:armhf (1.9.5-2) ...
Selecting previously unselected package libsmithwaterman0:armhf.
Preparing to unpack .../87-libsmithwaterman0_0.0+git20160702.2610e25-12_armhf.deb ...
Unpacking libsmithwaterman0:armhf (0.0+git20160702.2610e25-12) ...
Selecting previously unselected package libsmithwaterman-dev:armhf.
Preparing to unpack .../88-libsmithwaterman-dev_0.0+git20160702.2610e25-12_armhf.deb ...
Unpacking libsmithwaterman-dev:armhf (0.0+git20160702.2610e25-12) ...
Selecting previously unselected package sbuild-build-depends-tvc-dummy.
Preparing to unpack .../89-sbuild-build-depends-tvc-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-tvc-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.4.1-3) ...
Setting up libpipeline1:armhf (1.5.4-1) ...
Setting up cpp-11 (11.2.0-12+rpi1) ...
Setting up libdisorder0:armhf (0.0.2+git20130809.8062ee1-4) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up hdf5-helpers (1.10.7+repack-4+rpi1) ...
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.41-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libsmithwaterman0:armhf (0.0+git20160702.2610e25-12) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.41-2) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.41-2) ...
Setting up libgomp1:armhf (11.2.0-12+rpi1) ...
Setting up libaec0:armhf (1.0.6-1) ...
Setting up libasan6:armhf (11.2.0-12+rpi1) ...
Setting up gcc-10-base:armhf (10.3.0-13+rpi1) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libblas3:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libuv1:armhf (1.42.0-1) ...
Setting up libjpeg62-turbo:armhf (1:2.1.2-1) ...
Setting up emacsen-common (3.0.4) ...
Setting up libjpeg62-turbo-dev:armhf (1:2.1.2-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up dh-elpa-helper (2.0.9) ...
Setting up libncurses6:armhf (6.3-1) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-10) ...
Setting up libssl-dev:armhf (1.1.1l-1) ...
Setting up libatomic1:armhf (11.2.0-12+rpi1) ...
Setting up autopoint (0.21-4) ...
Setting up libjsoncpp25:armhf (1.9.5-2) ...
Setting up libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-4) ...
Setting up libgfortran5:armhf (11.2.0-12+rpi1) ...
Setting up libboost-math1.74.0:armhf (1.74.0-13) ...
Setting up libubsan1:armhf (11.2.0-12+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libgcc-11-dev:armhf (11.2.0-12+rpi1) ...
Setting up librhash0:armhf (1.4.2-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.10.0-2) ...
Setting up cmake-data (3.22.1-1) ...
Setting up libelf1:armhf (0.186-1) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libcc1-0:armhf (11.2.0-12+rpi1) ...
Setting up libprocps8:armhf (2:3.3.17-5) ...
Setting up libblas-dev:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libsz2:armhf (1.0.6-1) ...
Setting up libfile-stripnondeterminism-perl (1.12.1-1) ...
Setting up libjsoncpp-dev:armhf (1.9.5-2) ...
Setting up liblapack3:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up libarchive13:armhf (3.4.3-2) ...
Setting up libgcc-10-dev:armhf (10.3.0-13+rpi1) ...
Setting up libaec-dev:armhf (1.0.6-1) ...
Setting up libarpack2:armhf (3.8.0-1) ...
Setting up libjpeg-dev:armhf (1:2.1.2-1) ...
Setting up libsuperlu5:armhf (5.3.0+dfsg1-2) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libbamtools-dev:armhf (2.5.1+dfsg-10) ...
Setting up liblapack-dev:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libsmithwaterman-dev:armhf (0.0+git20160702.2610e25-12) ...
Setting up autoconf (2.71-2) ...
Setting up libstdc++-11-dev:armhf (11.2.0-12+rpi1) ...
Setting up dh-strip-nondeterminism (1.12.1-1) ...
Setting up dwz (0.14-1) ...
Setting up gcc-11 (11.2.0-12+rpi1) ...
Setting up groff-base (1.22.4-7) ...
Setting up procps (2:3.3.17-5) ...
Setting up libcurl4:armhf (7.79.1-2) ...
Setting up libsuperlu-dev:armhf (5.3.0+dfsg1-2) ...
Setting up automake (1:1.16.5-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libarmadillo10 (1:10.7.4+dfsg-1) ...
Setting up libarpack2-dev:armhf (3.8.0-1) ...
Setting up libstdc++-10-dev:armhf (10.3.0-13+rpi1) ...
Setting up libboost1.74-dev:armhf (1.74.0-13) ...
Setting up g++-11 (11.2.0-12+rpi1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up libcurl4-openssl-dev:armhf (7.79.1-2) ...
Setting up libhdf5-103-1:armhf (1.10.7+repack-4+rpi1) ...
Setting up libhdf5-cpp-103-1:armhf (1.10.7+repack-4+rpi1) ...
Setting up cmake (3.22.1-1+b1) ...
Setting up libboost-math1.74-dev:armhf (1.74.0-13) ...
Setting up libhdf5-hl-100:armhf (1.10.7+repack-4+rpi1) ...
Setting up libboost-math-dev:armhf (1.74.0.3+b2) ...
Setting up debhelper (13.5.2) ...
Setting up libhdf5-hl-cpp-100:armhf (1.10.7+repack-4+rpi1) ...
Setting up libhdf5-fortran-102:armhf (1.10.7+repack-4+rpi1) ...
Setting up libhdf5-hl-fortran-100:armhf (1.10.7+repack-4+rpi1) ...
Setting up libhdf5-dev (1.10.7+repack-4+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libarmadillo-dev (1:10.7.4+dfsg-1) ...
Setting up sbuild-build-depends-tvc-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-163-generic armhf (armv8l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-11_11.2.0-12+rpi1 gcc-11_11.2.0-12+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-13+rpi1 libstdc++-11-dev_11.2.0-12+rpi1 libstdc++6_11.2.0-12+rpi1 linux-libc-dev_5.14.16-1+rpi1
Package versions: adduser_3.118 apt_2.3.12 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3.1 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 cmake_3.22.1-1+b1 cmake-data_3.22.1-1 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-12+rpi1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-elpa-helper_2.0.9 dh-strip-nondeterminism_1.12.1-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 emacsen-common_3.0.4 fakeroot_1.25.3-1.1 file_1:5.41-2 findutils_4.8.0-1 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-12+rpi1 gcc_4:11.2.0-2+rpi1 gcc-10-base_10.3.0-13+rpi1 gcc-11_11.2.0-12+rpi1 gcc-11-base_11.2.0-12+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hdf5-helpers_1.10.7+repack-4+rpi1 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapt-pkg6.0_2.3.12 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libarmadillo-dev_1:10.7.4+dfsg-1 libarmadillo10_1:10.7.4+dfsg-1 libarpack2_3.8.0-1 libarpack2-dev_3.8.0-1 libasan6_11.2.0-12+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-12+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbamtools-dev_2.5.1+dfsg-10 libbamtools2.5.1_2.5.1+dfsg-10 libbinutils_2.37-5+rpi1 libblas-dev_3.10.0-1 libblas3_3.10.0-1 libblkid1_2.37.2-4 libboost-math-dev_1.74.0.3+b2 libboost-math1.74-dev_1.74.0-13 libboost-math1.74.0_1.74.0-13 libboost1.74-dev_1.74.0-13 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-12+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.26-1 libcrypt1_1:4.4.26-1 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl4_7.79.1-2 libcurl4-openssl-dev_7.79.1-2 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.5.2 libdisorder-dev_0.0.2+git20130809.8062ee1-4 libdisorder0_0.0.2+git20130809.8062ee1-4 libdpkg-perl_1.20.9+rpi1 libelf1_0.186-1 libexpat1_2.4.1-3 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.1-1 libgcc-10-dev_10.3.0-13+rpi1 libgcc-11-dev_11.2.0-12+rpi1 libgcc-s1_11.2.0-12+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgfortran5_11.2.0-12+rpi1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.2-2 libgomp1_11.2.0-12+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhdf5-103-1_1.10.7+repack-4+rpi1 libhdf5-cpp-103-1_1.10.7+repack-4+rpi1 libhdf5-dev_1.10.7+repack-4+rpi1 libhdf5-fortran-102_1.10.7+repack-4+rpi1 libhdf5-hl-100_1.10.7+repack-4+rpi1 libhdf5-hl-cpp-100_1.10.7+repack-4+rpi1 libhdf5-hl-fortran-100_1.10.7+repack-4+rpi1 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libjpeg-dev_1:2.1.2-1 libjpeg62-turbo_1:2.1.2-1 libjpeg62-turbo-dev_1:2.1.2-1 libjsoncpp-dev_1.9.5-2 libjsoncpp25_1.9.5-2 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 liblapack-dev_3.10.0-1 liblapack3_3.10.0-1 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libncurses6_6.3-1 libncursesw6_6.3-1 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libprocps8_2:3.3.17-5 libpsl5_0.21.0-1.2 libreadline8_8.1-2 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg2-2 libsasl2-modules-db_2.1.27+dfsg2-2 libseccomp2_2.5.3-2+rpi1 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsmithwaterman-dev_0.0+git20160702.2610e25-12 libsmithwaterman0_0.0+git20160702.2610e25-12 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl-dev_1.1.1l-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-13+rpi1 libstdc++-11-dev_11.2.0-12+rpi1 libstdc++6_11.2.0-12+rpi1 libsub-override-perl_0.09-2 libsuperlu-dev_5.3.0+dfsg1-2 libsuperlu5_5.3.0+dfsg1-2 libsystemd0_249.7-1+rpi1 libsz2_1.0.6-1 libtasn1-6_4.18.0-4 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.3-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-12+rpi1 libuchardet0_0.0.7-1 libudev1_249.7-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libuv1_1.42.0-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.16-1+rpi1 login_1:4.8.1-2 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-4 ncurses-base_6.3-1 ncurses-bin_6.3-1 netbase_6.3 passwd_1:4.8.1-2 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 procps_2:3.3.17-5 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tvc-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.GcWa7lYu/trustedkeys.kbx': General error
gpgv: Signature made Sun Oct 31 15:09:13 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./tvc_5.0.3+git20151221.80e144e+dfsg-4.dsc
dpkg-source: info: extracting tvc in /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg
dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz
dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying cmake.patch
dpkg-source: info: applying bamtools.patch
dpkg-source: info: applying help.patch
dpkg-source: info: applying hurd.patch
dpkg-source: info: applying sse.patch
dpkg-source: info: applying use_debian_packaged_smithwaterman.patch
dpkg-source: info: applying python3.patch
dpkg-source: info: applying gcc11.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 5.0.3+git20151221.80e144e+dfsg-4+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-19c77207-3dfd-4e3b-b5b3-a7bf93c072aa
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package tvc
dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-4+b1
dpkg-buildpackage: info: source distribution bookworm-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf ..
CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
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[ 7%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o
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[ 9%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o
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/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:9: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations]
36 | arma::set_stream_err1(null_ostream);
| ^~~~~~~~~~~~~~~
In file included from /usr/include/armadillo:357,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:92:1: note: declared here
92 | set_stream_err1(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations]
36 | arma::set_stream_err1(null_ostream);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/armadillo:357,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:92:1: note: declared here
92 | set_stream_err1(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:9: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations]
37 | arma::set_stream_err2(null_ostream);
| ^~~~~~~~~~~~~~~
In file included from /usr/include/armadillo:357,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:103:1: note: declared here
103 | set_stream_err2(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations]
37 | arma::set_stream_err2(null_ostream);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/armadillo:357,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:103:1: note: declared here
103 | set_stream_err2(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
[ 10%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o
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[ 12%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp
[ 14%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o
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[ 15%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp
[ 17%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp
[ 18%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 20%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o
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[ 21%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o
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[ 23%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -MF CMakeFiles/tvcassembly.dir/IonVersion.cpp.o.d -o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/IonVersion.cpp
[ 25%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HandleVariant.cpp
[ 26%] Linking CXX executable tvcassembly
/usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -o tvcassembly -lbamtools -lz -lpthread -ljsoncpp
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
[ 26%] Built target tvcassembly
[ 28%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp
[ 29%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HotspotReader.cpp
[ 31%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/MetricsManager.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:13:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator<markov_state>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<markov_state>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator<markov_state>]':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<markov_state*, std::vector<markov_state> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void markov_chain<T>::generate_states(T, T) [with T = unsigned int]':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<markov_state*, std::vector<markov_state> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 32%] Building CXX object CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 34%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/MiscUtil.cpp
[ 35%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp
[ 37%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp
[ 39%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/ExtendParameters.cpp
[ 40%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp
[ 42%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp
[ 43%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/VcfFormat.cpp
[ 45%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function 'ti_index_core':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow]
336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
| ^~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:12,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DPTreephaser&}; _Tp = DPTreephaser; _Alloc = std::allocator<DPTreephaser>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<DPTreephaser>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:12,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7:
/usr/include/c++/11/bits/stl_vector.h: In constructor 'PersistingThreadObjects::PersistingThreadObjects(const InputStructures&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DPTreephaser*, std::vector<DPTreephaser> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 46%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads/ExtendedReadInfo.cpp
[ 48%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ErrorMotifs.cpp
[ 50%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/LocalContext.cpp
[ 51%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
678 | fread(buf, 1, 28, fp->file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 53%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ClassifyVariant.cpp
[ 54%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/IonVersion.cpp.o -MF CMakeFiles/tvcutils.dir/IonVersion.cpp.o.d -o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/IonVersion.cpp
[ 56%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/SpliceVariantHypotheses.cpp
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make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
[ 59%] Built target tvcutils
[ 60%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector<float>&, std::vector<float>&, bool)':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:191:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<float>::size_type' {aka 'unsigned int'} [-Wformat=]
191 | fprintf(stdout, "ref.size()=%lu; ", ref.size());
| ~~^ ~~~~~~~~~~
| | |
| | std::vector<float>::size_type {aka unsigned int}
| long unsigned int
| %u
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:192:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<float>::size_type' {aka 'unsigned int'} [-Wformat=]
192 | fprintf(stdout, "var.size()=%lu; ", var.size());
| ~~^ ~~~~~~~~~~
| | |
| | std::vector<float>::size_type {aka unsigned int}
| long unsigned int
| %u
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:193:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wformat=]
193 | fprintf(stdout, "both.size()=%lu; ", both.size());
| ~~^ ~~~~~~~~~~~
| | |
| | std::vector<double>::size_type {aka unsigned int}
| long unsigned int
| %u
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[ 76%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp
[ 78%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/split.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/split.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp
[ 79%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp
[ 81%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function 'ti_index_core':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow]
336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
| ^~~~~~~~
[ 82%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
678 | fread(buf, 1, 28, fp->file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 84%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o
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[ 85%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o
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[ 87%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o
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[ 89%] Building CXX object CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o
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[ 90%] Building CXX object CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o
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[ 92%] Building CXX object CMakeFiles/tvc.dir/Util/OptArgs.cpp.o
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[ 95%] Building C object CMakeFiles/tvc.dir/file-io/ion_util.c.o
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In file included from /usr/include/c++/11/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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make[1]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
dh_auto_test -a
cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=--verbose ARGS\+=-j4
make[1]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
Running tests...
/usr/bin/ctest --force-new-ctest-process --verbose -j4
UpdateCTestConfiguration from :/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl
Test project /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: tvc_call
1: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc
1: Test timeout computed to be: 10000000
test 2
Start 2: tvc_test_1_thread_sse_off
2: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc "--input-bam" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/test1" "--output-vcf" "small_variants.vcf"
2: Test timeout computed to be: 10000000
test 3
Start 3: tvc_test_4_threads_sse_off_with_parameter_file
3: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc "--input-bam" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/test2" "--output-vcf" "small_variants.vcf"
3: Test timeout computed to be: 10000000
test 4
Start 4: tvcutils_call
4: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils
4: Test timeout computed to be: 10000000
1: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
1:
1: Usage: tvc [options]
1:
1: General options:
1: -h,--help print this help message and exit
1: -v,--version print version and exit
1: -n,--num-threads INT number of worker threads [2]
1: -N,--num-variants-per-thread INT worker thread batch size [500]
1: --parameters-file FILE json file with algorithm control parameters [optional]
1:
1: Inputs:
1: -r,--reference FILE reference fasta file [required]
1: -b,--input-bam FILE bam file with mapped reads [required]
1: -g,--sample-name STRING sample for which variants are called (In case of input BAM files with multiple samples) [optional if there is only one sample]
1: --force-sample-name STRING force all read groups to have this sample name [off]
1: -t,--target-file FILE only process targets in this bed file [optional]
1: --trim-ampliseq-primers on/off match reads to targets and trim the ends that reach outside them [off]
1: -D,--downsample-to-coverage INT ?? [2000]
1: --model-file FILE HP recalibration model input file.
1: --recal-model-hp-thres INT Lower threshold for HP recalibration.
1:
1: Outputs:
1: -O,--output-dir DIRECTORY base directory for all output files [current dir]
1: -o,--output-vcf FILE vcf file with variant calling results [required]
1: --suppress-reference-genotypes on/off write reference calls into the filtered variants vcf [on]
1: --suppress-no-calls on/off write filtered variants into the filtered variants vcf [on]
1: --suppress-nocall-genotypes on/off do not report a genotype for filtered variants [on]
1:
1: Variant candidate generation (FreeBayes):
1: --allow-snps on/off allow generation of snp candidates [on]
1: --allow-indels on/off allow generation of indel candidates [on]
1: --allow-mnps on/off allow generation of mnp candidates [on]
1: --allow-complex on/off allow generation of block substitution candidates [off]
1: --max-complex-gap INT maximum number of reference alleles between two alternate alleles to allow merging of the alternate alleles [1]
1: -m,--use-best-n-alleles INT maximum number of snp alleles [2]
1: -M,--min-mapping-qv INT do not use reads with mapping quality below this [4]
1: -U,--read-snp-limit INT do not use reads with number of snps above this [10]
1: -z,--read-max-mismatch-fraction FLOAT do not use reads with fraction of mismatches above this [1.0]
1: --gen-min-alt-allele-freq FLOAT minimum required alt allele frequency to generate a candidate [0.2]
1: --gen-min-indel-alt-allele-freq FLOAT minimum required alt allele frequency to generate a homopolymer indel candidate [0.2]
1: --gen-min-coverage INT minimum required coverage to generate a candidate [6]
1:
1: External variant candidates:
1: -c,--input-vcf FILE vcf.gz file (+.tbi) with additional candidate variant locations and alleles [optional]
1: --process-input-positions-only on/off only generate candidates at locations from input-vcf [off]
1: --use-input-allele-only on/off only consider provided alleles for locations in input-vcf [off]
1:
1: Variant candidate scoring options:
1: --min-delta-for-flow FLOAT minimum prediction delta for scoring flows [0.1]
1: --max-flows-to-test INT maximum number of scoring flows [10]
1: --outlier-probability FLOAT probability for outlier reads [0.01]
1: --heavy-tailed INT degrees of freedom in t-dist modeling signal residual heavy tail [3]
1: --suppress-recalibration on/off Suppress homopolymer recalibration [on].
1: --do-snp-realignment on/off Realign reads in the vicinity of candidate snp variants [on].
1: --do-mnp-realignment on/off Realign reads in the vicinity of candidate mnp variants [do-snp-realignment].
1: --realignment-threshold FLOAT Max. allowed fraction of reads where realignment causes an alignment change [1.0].
1:
1: Advanced variant candidate scoring options:
1: --use-sse-basecaller on/off Switch to use the vectorized version of the basecaller [off].
1: --resolve-clipped-bases on/off If 'true', the basecaller is used to solve soft clipped bases [off].
1: --prediction-precision FLOAT prior weight in bias estimator [30.0]
1: --shift-likelihood-penalty FLOAT penalize log-likelihood for solutions involving large systematic bias [0.3]
1: --minimum-sigma-prior FLOAT prior variance per data point, constant [0.085]
1: --slope-sigma-prior FLOAT prior rate of increase of variance over minimum by signal [0.0084]
1: --sigma-prior-weight FLOAT weight of prior estimate of variance compared to observations [1.0]
1: --k-zero FLOAT variance increase for adding systematic bias [3.0]
1: --sse-relative-safety-level FLOAT dampen strand bias detection for SSE events for low coverage [0.025]
1: --tune-sbias FLOAT dampen strand bias detection for low coverage [0.01]
1: --max-detail-level INT number of evaluated frequencies for a given hypothesis, reduce for very high coverage, set to zero to disable this option [0]
1:
1: Variant filtering:
1: -k,--snp-min-coverage INT filter out snps with total coverage below this [6]
1: -C,--snp-min-cov-each-strand INT filter out snps with coverage on either strand below this [0]
1: -B,--snp-min-variant-score FLOAT filter out snps with QUAL score below this [10.0]
1: -s,--snp-strand-bias FLOAT filter out snps with strand bias above this [0.95] given pval < snp-strand-bias-pval
1: --snp-strand-bias-pval FLOAT filter out snps with pval below this [1.0] given strand bias > snp-strand-bias
1: -A,--snp-min-allele-freq FLOAT minimum required alt allele frequency for non-reference snp calls [0.2]
1: --mnp-min-coverage INT filter out mnps with total coverage below this [snp-min-coverage]
1: --mnp-min-cov-each-strand INT filter out mnps with coverage on either strand below this, [snp-min-cov-each-strand]
1: --mnp-min-variant-score FLOAT filter out mnps with QUAL score below this [snp-min-variant-score]
1: --mnp-strand-bias FLOAT filter out mnps with strand bias above this [snp-strand-bias] given pval < mnp-strand-bias-pval
1: --mnp-strand-bias-pval FLOAT filter out mnps with pval below this [snp-strand-bias-pval] given strand bias > mnp-strand-bias
1: --mnp-min-allele-freq FLOAT minimum required alt allele frequency for non-reference mnp calls [snp-min-allele-freq]
1: --indel-min-coverage INT filter out indels with total coverage below this [30]
1: --indel-min-cov-each-strand INT filter out indels with coverage on either strand below this [1]
1: --indel-min-variant-score FLOAT filter out indels with QUAL score below this [10.0]
1: -S,--indel-strand-bias FLOAT filter out indels with strand bias above this [0.95] given pval < indel-strand-bias-pval
1: --indel-strand-bias-pval FLOAT filter out indels with pval below this [1.0] given strand bias > indel-strand-bias
1: --indel-min-allele-freq FLOAT minimum required alt allele frequency for non-reference indel call [0.2]
1: --hotspot-min-coverage INT filter out hotspot variants with total coverage below this [6]
1: --hotspot-min-cov-each-strand INT filter out hotspot variants with coverage on either strand below this [snp-min-cov-each-strand]
1: --hotspot-min-variant-score FLOAT filter out hotspot variants with QUAL score below this [snp-min-variant-score]
1: --hotspot-strand-bias FLOAT filter out hotspot variants with strand bias above this [0.95] given pval < hotspot-strand-bias-pval
1: --hotspot-strand-bias-pval FLOAT filter out hotspot variants with pval below this [1.0] given strand bias > hotspot-strand-bias
1: -H,--hotspot-min-allele-freq FLOAT minimum required alt allele frequency for non-reference hotspot variant call [0.2]
1: -L,--hp-max-length INT filter out indels in homopolymers above this [8]
1: -e,--error-motifs FILE table of systematic error motifs and their error rates [optional]
1: --sse-prob-threshold FLOAT filter out variants in motifs with error rates above this [0.2]
1: --min-ratio-reads-non-sse-strand FLOAT minimum required alt allele frequency for variants with error motifs on opposite strand [0.2]
1: --indel-as-hpindel on/off apply indel filters to non HP indels [off]
1:
1: Position bias variant filtering:
1: --use-position-bias on/off enable the position bias filter [off]
1: --position-bias FLOAT filter out variants with position bias relative to soft clip ends in reads > position-bias [0.75]
1: --position-bias-pval FLOAT filter out if position bias above position-bias given pval < position-bias-pval [0.05]
1: --position-bias-ref-fraction FLOAT skip position bias filter if (reference read count)/(reference + alt allele read count) <= to this [0.05]
1:
1: Filters that depend on scoring across alleles:
1: --data-quality-stringency FLOAT minimum mean log-likelihood delta per read [4.0]
1: --read-rejection-threshold FLOAT filter variants where large numbers of reads are rejected as outliers [0.5]
1: --filter-unusual-predictions FLOAT posterior log likelihood threshold for accepting bias estimate [0.3]
1: --filter-deletion-predictions FLOAT check post-evaluation systematic bias in deletions; a high value like 100 effectively turns off this filter [100.0]
1: --filter-insertion-predictions FLOAT check post-evaluation systematic bias in insertions; a high value like 100 effectively turns off this filter [100.0]
1:
1: --heal-snps on/off suppress in/dels not participating in diploid variant genotypes if the genotype contains a SNP or MNP [on].
1:
1: Debugging:
1: -d,--debug INT (0/1/2) display extra debug messages [0]
1: --do-json-diagnostic on/off (devel) dump internal state to json file (uses much more time/memory/disk) [off]
1: --postprocessed-bam FILE (devel) save tvc-processed reads to an (unsorted) BAM file [optional]
1: --do-minimal-diagnostic on/off (devel) provide minimal read information for called variants [off]
1: --override-limits on/off (devel) disable limit-check on input parameters [off].
1:
2: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
2:
2: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf
2: hp-max-length = 8 (integer, builtin default)
2: sse-prob-threshold = 0.2 (double, builtin default)
2: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default)
2: sse-relative-safety-level = 0.025 (double, builtin default)
1/8 Test #1: tvc_call ......................................... Passed 0.01 sec
test 5
Start 5: tvcutils_prepare_hotspots_call
5: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "prepare_hotspots"
5: Test timeout computed to be: 10000000
2: do-snp-realignment = true (boolean, builtin default)
2: do-mnp-realignment = true (boolean, builtin default)
2: realignment-threshold = 1 (double, builtin default)
2: indel-as-hpindel = false (boolean, builtin default)
2: data-quality-stringency = 4 (double, builtin default)
2: read-rejection-threshold = 0.5 (double, builtin default)
2: use-position-bias = false (boolean, builtin default)
2: position-bias-ref-fraction = 0.05 (double, builtin default)
2: position-bias = 0.75 (double, builtin default)
2: position-bias-pval = 0.05 (double, builtin default)
2: downsample-to-coverage = 2000 (integer, builtin default)
2: tune-sbias = 0.01 (double, builtin default)
2: suppress-reference-genotypes = true (boolean, builtin default)
2: suppress-nocall-genotypes = true (boolean, builtin default)
2: suppress-no-calls = true (boolean, builtin default)
2: heal-snps = true (boolean, builtin default)
2: snp-min-cov-each-strand = 0 (integer, builtin default)
2: snp-min-variant-score = 10 (double, builtin default)
2: snp-min-allele-freq = 0.2 (double, builtin default)
2: snp-min-coverage = 6 (integer, builtin default)
2: snp-strand-bias = 0.95 (double, builtin default)
2: snp-strand-bias-pval = 1 (double, builtin default)
2: mnp-min-cov-each-strand = 0 (integer, builtin default)
2: mnp-min-variant-score = 10 (double, builtin default)
2: mnp-min-allele-freq = 0.2 (double, builtin default)
2: mnp-min-coverage = 6 (integer, builtin default)
2: mnp-strand-bias = 0.95 (double, builtin default)
2: mnp-strand-bias-pval = 1 (double, builtin default)
2: indel-min-cov-each-strand = 1 (integer, builtin default)
2: indel-min-variant-score = 10 (double, builtin default)
2: indel-min-allele-freq = 0.2 (double, builtin default)
2: indel-min-coverage = 15 (integer, builtin default)
2: indel-strand-bias = 0.85 (double, builtin default)
2: indel-strand-bias-pval = 1 (double, builtin default)
2: hotspot-min-cov-each-strand = 0 (integer, builtin default)
2: hotspot-min-variant-score = 10 (double, builtin default)
2: hotspot-min-allele-freq = 0.2 (double, builtin default)
2: hotspot-min-coverage = 6 (integer, builtin default)
2: hotspot-strand-bias = 0.95 (double, builtin default)
2: hotspot-strand-bias-pval = 1 (double, builtin default)
2: max-flows-to-test = 10 (integer, builtin default)
2: min-delta-for-flow = 0.1 (double, builtin default)
2: prediction-precision = 30 (double, builtin default)
2: outlier-probability = 0.01 (double, builtin default)
2: germline-prior-strength = 0 (double, builtin default)
2: heavy-tailed = 3 (integer, builtin default)
2: filter-unusual-predictions = 0.3 (double, builtin default)
2: soft-clip-bias-checker = 0.1 (double, builtin default)
2: filter-deletion-predictions = 100 (double, builtin default)
2: filter-insertion-predictions = 100 (double, builtin default)
2: max-detail-level = 0 (integer, builtin default)
2: shift-likelihood-penalty = 0.3 (double, builtin default)
2: minimum-sigma-prior = 0.085 (double, builtin default)
2: slope-sigma-prior = 0.0084 (double, builtin default)
2: sigma-prior-weight = 1 (double, builtin default)
2: k-zero = 3 (double, builtin default)
2: num-threads = 1 (integer, command line option)
2: num-variants-per-thread = 250 (integer, builtin default)
2: use-sse-basecaller = false (boolean, command line option)
2: do-json-diagnostic = false (boolean, builtin default)
2: do-minimal-diagnostic = false (boolean, builtin default)
2: process-input-positions-only = false (boolean, builtin default)
2: suppress-recalibration = true (boolean, builtin default)
2: resolve-clipped-bases = false (boolean, builtin default)
2: prefix-exclude = 6
2: allow-indels = true (boolean, builtin default)
2: allow-snps = true (boolean, builtin default)
2: allow-mnps = true (boolean, builtin default)
2: allow-complex = false (boolean, builtin default)
2: left-align-indels = false (boolean, builtin default)
2: use-best-n-alleles = 2 (integer, builtin default)
2: use-input-allele-only = false (boolean, builtin default)
2: min-mapping-qv = 4 (integer, builtin default)
2: read-snp-limit = 10 (integer, builtin default)
2: read-max-mismatch-fraction = 1 (double, builtin default)
2: max-complex-gap = 1 (integer, builtin default)
2: gen-min-alt-allele-freq = 0.2 (double, builtin default)
2: gen-min-coverage = 6 (integer, builtin default)
2: gen-min-indel-alt-allele-freq = 0.2 (double, builtin default)
2: override-limits = false (boolean, builtin default)
2: Limit check parameter hp-max-length: lim. 1 <= 8? OK!
2: Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK!
2: Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter data-quality-stringency: lim. 0 <= 4? OK!
2: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK!
2: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK!
2: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK!
2: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK!
2: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK!
2: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK!
2: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK!
2: Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK!
2: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter snp-min-coverage: lim. 0 <= 6? OK!
2: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
2: Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK!
2: Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK!
2: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK!
2: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
2: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK!
2: Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK!
2: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter indel-min-coverage: lim. 0 <= 15? OK!
2: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK!
2: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK!
2: Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK!
2: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK!
2: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
2: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK!
2: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK!
2: Limit check parameter prediction-precision: lim. 0.1 <= 30? OK!
2: Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK!
2: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK!
2: Limit check parameter heavy-tailed: lim. 1 <= 3? OK!
2: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK!
2: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK!
2: Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK!
2: Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK!
2: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK!
2: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK!
2: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK!
2: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK!
2: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK!
2: Limit check parameter k-zero: lim. 0 <= 3? OK!
2: Limit check parameter num-threads: lim. 1 <= 1 <= lim. 128? OK!
2: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK!
2: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK!
2: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK!
2: Limit check parameter read-snp-limit: lim. 0 <= 10? OK!
2: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK!
2: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
4:
4: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
4:
4: Usage: tvcutils <command> [options]
4:
4: Commands:
4: prepare_hotspots Convert BED or VCF file into a valid hotspot file
4: validate_bed Validate targets or hotspots file
4: unify_vcf Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots)
4:
3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
3:
3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf
3: hp-max-length = 8 (integer, parameters json file)
3: sse-prob-threshold = 1 (double, parameters json file)
3: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default)
3: sse-relative-safety-level = 0.025 (double, builtin default)
3: do-snp-realignment = false (boolean, parameters json file)
3: do-mnp-realignment = false (boolean, parameters json file)
3: realignment-threshold = 0 (double, parameters json file)
3: indel-as-hpindel = false (boolean, parameters json file)
3: data-quality-stringency = 10 (double, parameters json file)
3: read-rejection-threshold = 0.5 (double, builtin default)
3: use-position-bias = false (boolean, parameters json file)
3: position-bias-ref-fraction = 0.05 (double, parameters json file)
3: position-bias = 0.75 (double, parameters json file)
3: position-bias-pval = 0.05 (double, parameters json file)
3: downsample-to-coverage = 2000 (integer, parameters json file)
3: tune-sbias = 0.01 (double, builtin default)
3: suppress-reference-genotypes = true (boolean, builtin default)
3: suppress-nocall-genotypes = true (boolean, builtin default)
3: suppress-no-calls = true (boolean, builtin default)
3: heal-snps = true (boolean, builtin default)
3: snp-min-cov-each-strand = 4 (integer, parameters json file)
3: snp-min-variant-score = 6 (double, parameters json file)
3: snp-min-allele-freq = 0.02 (double, parameters json file)
3: snp-min-coverage = 100 (integer, parameters json file)
3: snp-strand-bias = 0.95 (double, parameters json file)
3: snp-strand-bias-pval = 0.01 (double, parameters json file)
3: mnp-min-cov-each-strand = 4 (integer, parameters json file)
3: mnp-min-variant-score = 6 (double, parameters json file)
3: mnp-min-allele-freq = 0.02 (double, parameters json file)
3: mnp-min-coverage = 100 (integer, parameters json file)
3: mnp-strand-bias = 0.95 (double, parameters json file)
3: mnp-strand-bias-pval = 0.01 (double, parameters json file)
3: indel-min-cov-each-strand = 4 (integer, parameters json file)
3: indel-min-variant-score = 6 (double, parameters json file)
3: indel-min-allele-freq = 0.02 (double, parameters json file)
3: indel-min-coverage = 100 (integer, parameters json file)
3: indel-strand-bias = 0.9 (double, parameters json file)
3: indel-strand-bias-pval = 1 (double, parameters json file)
3: hotspot-min-cov-each-strand = 4 (integer, parameters json file)
3: hotspot-min-variant-score = 6 (double, parameters json file)
3: hotspot-min-allele-freq = 0.02 (double, parameters json file)
3: hotspot-min-coverage = 100 (integer, parameters json file)
3: hotspot-strand-bias = 0.95 (double, parameters json file)
3: hotspot-strand-bias-pval = 0.01 (double, parameters json file)
3: max-flows-to-test = 10 (integer, builtin default)
3: min-delta-for-flow = 0.1 (double, builtin default)
3: prediction-precision = 1 (double, parameters json file)
3: outlier-probability = 0.005 (double, parameters json file)
3: germline-prior-strength = 0 (double, builtin default)
3: heavy-tailed = 3 (integer, parameters json file)
3: filter-unusual-predictions = 0.12 (double, parameters json file)
3: soft-clip-bias-checker = 0.1 (double, builtin default)
3: filter-deletion-predictions = 0.2 (double, parameters json file)
3: filter-insertion-predictions = 0.2 (double, parameters json file)
3: max-detail-level = 0 (integer, builtin default)
3: shift-likelihood-penalty = 0.3 (double, builtin default)
3: minimum-sigma-prior = 0.085 (double, builtin default)
3: slope-sigma-prior = 0.0084 (double, builtin default)
3: sigma-prior-weight = 1 (double, builtin default)
3: k-zero = 3 (double, builtin default)
3: num-threads = 4 (integer, command line option)
3: num-variants-per-thread = 250 (integer, builtin default)
3: use-sse-basecaller = false (boolean, command line option)
3: do-json-diagnostic = false (boolean, builtin default)
3: do-minimal-diagnostic = false (boolean, builtin default)
3: process-input-positions-only = false (boolean, builtin default)
3: suppress-recalibration = false (boolean, parameters json file)
3: resolve-clipped-bases = false (boolean, builtin default)
3: prefix-exclude = 6
3: allow-indels = true (boolean, parameters json file)
3: allow-snps = true (boolean, parameters json file)
3: allow-mnps = true (boolean, parameters json file)
3: allow-complex = false (boolean, parameters json file)
3: left-align-indels = false (boolean, builtin default)
3: use-best-n-alleles = 2 (integer, builtin default)
3: use-input-allele-only = false (boolean, builtin default)
3: min-mapping-qv = 4 (integer, parameters json file)
3: read-snp-limit = 10 (integer, parameters json file)
3: read-max-mismatch-fraction = 1 (double, parameters json file)
3: max-complex-gap = 1 (integer, builtin default)
3: gen-min-alt-allele-freq = 0.01 (double, parameters json file)
3: gen-min-coverage = 6 (integer, parameters json file)
3: gen-min-indel-alt-allele-freq = 0.01 (double, parameters json file)
3: override-limits = false (boolean, builtin default)
3: Limit check parameter hp-max-length: lim. 1 <= 8? OK!
3: Limit check parameter sse-prob-threshold: lim. 0 <= 1 <= lim. 1? OK!
3: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK!
3: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK!
3: Limit check parameter realignment-threshold: lim. 0 <= 0 <= lim. 1? OK!
3: Limit check parameter data-quality-stringency: lim. 0 <= 10? OK!
3: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK!
3: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK!
3: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK!
3: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK!
3: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK!
3: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK!
3: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 4? OK!
3: Limit check parameter snp-min-variant-score: lim. 0 <= 6? OK!
3: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK!
3: Limit check parameter snp-min-coverage: lim. 0 <= 100? OK!
3: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
3: Limit check parameter snp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK!
3: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 4? OK!
3: Limit check parameter mnp-min-variant-score: lim. 0 <= 6? OK!
3: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK!
3: Limit check parameter mnp-min-coverage: lim. 0 <= 100? OK!
3: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
3: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK!
3: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 4? OK!
2/8 Test #4: tvcutils_call .................................... Passed 0.01 sec
test 6
Start 6: tvcutils_validate_bed_call
6: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "validate_bed"
6: Test timeout computed to be: 10000000
2: TargetsManager: Loaded targets file /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed
2: TargetsManager: 1 target(s)
2: TargetsManager: Trimming of AmpliSeq primers is enabled
2: SampleManager: Found 1 read group(s) and 1 sample(s).
2: SampleManager: Primary sample "85" (default) present in 1 read group(s)
2: TVC found a total of 1 different flow orders of max flow lengths: 500
3: Limit check parameter indel-min-variant-score: lim. 0 <= 6? OK!
3: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK!
3: Limit check parameter indel-min-coverage: lim. 0 <= 100? OK!
3: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.9 <= lim. 1? OK!
3: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK!
3: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 4? OK!
3: Limit check parameter hotspot-min-variant-score: lim. 0 <= 6? OK!
3: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK!
3: Limit check parameter hotspot-min-coverage: lim. 0 <= 100? OK!
3: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
3: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK!
3: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK!
3: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK!
3: Limit check parameter prediction-precision: lim. 0.1 <= 1? OK!
3: Limit check parameter outlier-probability: lim. 0 <= 0.005 <= lim. 1? OK!
3: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK!
3: Limit check parameter heavy-tailed: lim. 1 <= 3? OK!
3: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.12? OK!
3: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK!
3: Limit check parameter filter-deletion-predictions: lim. 0 <= 0.2? OK!
3: Limit check parameter filter-insertion-predictions: lim. 0 <= 0.2? OK!
3: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK!
3: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK!
3: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK!
3: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK!
3: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK!
3: Limit check parameter k-zero: lim. 0 <= 3? OK!
3: Limit check parameter num-threads: lim. 1 <= 4 <= lim. 128? OK!
3: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK!
3: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK!
3: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK!
3: Limit check parameter read-snp-limit: lim. 0 <= 10? OK!
3: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK!
3: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK!
3: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK!
3: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK!
3: TargetsManager: Loaded targets file /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed
3: TargetsManager: 1 target(s)
3: TargetsManager: Trimming of AmpliSeq primers is enabled
3: SampleManager: Found 1 read group(s) and 1 sample(s).
3: SampleManager: Primary sample "85" (default) present in 1 read group(s)
3: TVC found a total of 1 different flow orders of max flow lengths: 500
5:
5: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
5:
5: Usage: tvcutils prepare_hotspots [options]
5:
5: General options:
5: -b,--input-bed FILE input is a hotspots BED file (either -b or -v required)
5: -v,--input-vcf FILE input is a hotspots VCF file (either -b or -v required)
5: -d,--output-bed FILE output left-aligned hotspots in BED format [none]
5: -o,--output-vcf FILE output is a hotspots VCF file. To be used as input to --hotspot-vcf argument of variant_caller_pipeline.py (recommended) [none]
5: -r,--reference FILE FASTA file containing reference genome (required)
5: -a,--left-alignment on/off perform left-alignment of indels [off]
5: -s,--allow-block-substitutions on/off do not filter out block substitution hotspots [on]
5: -u,--unmerged-bed FILE input a target bed file to filter out hotspots that contain a junction of 2 amplicons (optional)
5:
3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.01 sec
test 7
Start 7: tvcutils_unify_vcf_call
7: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "unify_vcf"
7: Test timeout computed to be: 10000000
6:
6: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
6:
6: Usage: tvcutils validate_bed [options]
6:
6: Input selection options (must provide one):
6: --target-regions-bed FILE input is a target regions BED file (required)
6: --hotspots-bed FILE input is a hotspots BED file (required)
6:
6: General options:
6: --reference FILE FASTA file containing reference genome (required)
6: --validation-log FILE log file for user-readable warning/error messages [stdout]
6: --meta-json FILE save validation and file statistics to json file [none]
6: --unmerged-detail-bed FILE output a valid unmerged BED. To be used as input to --primer-trim-bed argument of variant_caller_pipeline.py (recommended) [none]
6: --unmerged-plain-bed FILE output a valid merged BED. To be used as input to --region-bed argument of variant_caller_pipeline.py (recommended) [none]
6: --merged-detail-bed FILE output an (almost) valid bedDetail merged BED [none]
6: --merged-plain-bed FILE output a valid plain merged BED [none]
6: --effective-bed FILE output a valid effective BED [none]
6:
4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.01 sec
test 8
Start 8: tvcassembly_call
8: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcassembly
8: Test timeout computed to be: 10000000
7: Parameter novel-tvc-vcf is required and empty.
7:
7: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
7:
7: Usage: tvcutils unify_vcf [options]
7:
7: General options:
7: -t,--novel-tvc-vcf FILE small variants VCF file produced by TVC (required)
7: -i,--novel-assembly-vcf FILE long indels VCF file produced by TVCASSEMBLY (optional)
7: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional)
7: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional)
7: -f,--reference-fasta FILE FASTA file containing reference genome (required)
7: -b,--target-file FILE target regions BED file (optional)
7: -o,--output-vcf FILE output merged and annotated VCF or VCF.GZ file (required)
7: -j,--tvc-metrics FILE JSON file with tvc metrics (optional)
7: -d,--input-depth FILE output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok)
7: -m,--min-depth INT minimum coverage depth in GVCF output (optional)
7:
5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.01 sec
8: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly
8:
8: Usage: tvcassembly [options]
8:
8: General options:
8: -h,--help print this help message and exit
8: -v,--version print version and exit
8: -n,--num-threads INT number of worker threads [2]
8: --parameters-file FILE json file with algorithm control parameters [optional]
8: -r,--reference FILE reference fasta file [required]
8: -b,--input-bam FILE bam file with mapped reads [required]
8: -t,--target-file FILE only process targets in this bed file [optional]
8: -o,--output-vcf FILE vcf file with variant calling results [required]
8: -g,--sample-name STRING sample for which variants are called (In case of input BAM files with multiple samples) [optional if there is only one sample]
8: --force-sample-name STRING force all read groups to have this sample name [off]
8:
8: --kmer_len INT (klen) Size of the smallest k-mer used in assembly [19].
8: --min_var_count INT (mincount) Minimum support for a variant to be evaluated [5].
8: --short_suffix_match INT (ssm) Minimum sequence match on both sides of the variant [5].
8: --min_indel_size INT (mis) Minimum size indel reported by assembly [4].
8: --max_hp_length INT (maxhp) Variants containing HP larger than this are not reported [8].
8: --min_var_freq FLOAT (minfreq) Minimum frequency of the variant to be reported [0.15].
8: --min_var_score FLOAT (minscore) Minimum score of the variant to be reported [10].
8: --relative_strand_bias FLOAT (stbias) Variants with strand bias above this are not reported [0.80].
8: --output_mnv INT (mnv) Output multi-nucleotide variants assembled in a region with multiple adjacent variants [0].
8:
6/8 Test #8: tvcassembly_call ................................. Passed 0.01 sec
2: Recalibration was detected from comment lines in bam file(s):
2: 1 unique blocks of recalibration info detected.
2: Loading systematic error contexts.
3: Recalibration was detected from comment lines in bam file(s):
3: 1 unique blocks of recalibration info detected.
3: Loading systematic error contexts.
2: Loaded.
3: Loaded.
2: Recalibration model: suppressed
2:
2:
2: [tvc] Normal termination. Processing time: 2 seconds.
3:
3:
3: [tvc] Normal termination. Processing time: 2 seconds.
7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 3.15 sec
8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 3.23 sec
100% tests passed, 0 tests failed out of 8
Total Test time (real) = 3.24 sec
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[100%] Built target tvc
make[2]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed
make[1]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
dh_installdocs -a
dh_installchangelogs -a
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcutils contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcassembly 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/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc were not linked against libdisorder.so.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc debian/tvc/usr/bin/tvcassembly were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_armhf.deb'.
dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_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 2021-12-15T23:18:59Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_armhf.changes:
------------------------------------------------------
Format: 1.8
Date: Sun, 31 Oct 2021 20:30:30 +0530
Source: tvc (5.0.3+git20151221.80e144e+dfsg-4)
Binary: tvc tvc-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 5.0.3+git20151221.80e144e+dfsg-4+b1
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
tvc - genetic variant caller for Ion Torrent sequencing platforms
Changes:
tvc (5.0.3+git20151221.80e144e+dfsg-4+b1) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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86f4153f81154e720455b118b361384e072d173a 7652 tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_armhf.buildinfo
ebcf768c3e83db55ef63cc29d23d8188c0ddc8ea 939304 tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_armhf.deb
Checksums-Sha256:
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49326facf17cd6b2c8070f32f9c8fa18b24917dc177e7051fd0e396d9a1d28e6 7652 tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_armhf.buildinfo
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Files:
0f1ed1b0a389ff19cedfb28087caf34e 10895432 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b1_armhf.deb
fb092cdcb3d964248d2ee36e4d431eed 7652 science optional tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_armhf.buildinfo
28343b3425c85891167a2a65f5740111 939304 science optional tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b1_armhf.deb
--------------------------------------------------------
new Debian package, version 2.0.
size 10895432 bytes: control archive=720 bytes.
529 bytes, 12 lines control
401 bytes, 4 lines md5sums
Package: tvc-dbgsym
Source: tvc (5.0.3+git20151221.80e144e+dfsg-4)
Version: 5.0.3+git20151221.80e144e+dfsg-4+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10951
Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-4+b1)
Section: debug
Priority: optional
Description: debug symbols for tvc
Build-Ids: 6de1e22e86c3c0a6fd767036e60c9e080873e574 c077690fce2901af670e96ee1ab3ea15002a7567 f1cbd004e71a4e69f84f8e99e58ce84381103258
drwxr-xr-x root/root 0 2021-10-31 15:00 ./
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.build-id/6d/
-rw-r--r-- root/root 2250308 2021-10-31 15:00 ./usr/lib/debug/.build-id/6d/e1e22e86c3c0a6fd767036e60c9e080873e574.debug
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.build-id/c0/
-rw-r--r-- root/root 7668420 2021-10-31 15:00 ./usr/lib/debug/.build-id/c0/77690fce2901af670e96ee1ab3ea15002a7567.debug
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.build-id/f1/
-rw-r--r-- root/root 801652 2021-10-31 15:00 ./usr/lib/debug/.build-id/f1/cbd004e71a4e69f84f8e99e58ce84381103258.debug
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 477308 2021-10-31 15:00 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/tvc.debug
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-31 15:00 ./usr/share/doc/tvc-dbgsym -> tvc
tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_armhf.deb
-------------------------------------------------
new Debian package, version 2.0.
size 939304 bytes: control archive=1724 bytes.
1044 bytes, 17 lines control
2537 bytes, 29 lines md5sums
Package: tvc
Source: tvc (5.0.3+git20151221.80e144e+dfsg-4)
Version: 5.0.3+git20151221.80e144e+dfsg-4+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2962
Depends: libarmadillo10 (>= 1:10.7.4+dfsg), libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.29), libdisorder0 (>= 0.0.2), libgcc-s1 (>= 3.5), libjsoncpp25 (>= 1.9.5), libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 11), zlib1g (>= 1:1.1.4), python3
Section: science
Priority: optional
Homepage: http://ioncommunity.thermofisher.com
Description: genetic variant caller for Ion Torrent sequencing platforms
Torrent Variant Caller (TVC) is a genetic variant caller for
Ion Torrent sequencing platforms, and is specially optimized to exploit the
underlying flow signal information in the statistical model
to evaluate variants. Torrent Variant Caller is designed to call
single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs),
insertions, deletions, and block substitutions.
drwxr-xr-x root/root 0 2021-10-31 15:00 ./
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/bin/
-rwxr-xr-x root/root 921632 2021-10-31 15:00 ./usr/bin/tvc
-rwxr-xr-x root/root 174404 2021-10-31 15:00 ./usr/bin/tvcassembly
-rwxr-xr-x root/root 485968 2021-10-31 15:00 ./usr/bin/tvcutils
-rwxr-xr-x root/root 12985 2021-10-31 15:00 ./usr/bin/variant_caller_pipeline.py
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/examples/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/examples/example1/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/examples/example1/expected/
-rw-r--r-- root/root 6876 2015-12-21 20:38 ./usr/share/TVC/examples/example1/expected/TSVC_variants.vcf
-rw-r--r-- root/root 6479 2015-12-21 20:38 ./usr/share/TVC/examples/example1/expected/small_variants.vcf
-rw-r--r-- root/root 108 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.dict
-rw-r--r-- root/root 3400 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.fasta
-rw-r--r-- root/root 22 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.fasta.fai
-rw-r--r-- root/root 225904 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bam
-rw-r--r-- root/root 96 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bam.bai
-rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bed
-rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_merged_plain.bed
-rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_original.bed
-rw-r--r-- root/root 70 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_unmerged_detail.bed
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/pluginMedia/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/pluginMedia/parameter_sets/
-rw-r--r-- root/root 2809 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2926 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2826 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json
-rw-r--r-- root/root 2918 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json
-rw-r--r-- root/root 3062 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2628 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2757 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/sse/
-rw-r--r-- root/root 683778 2015-12-21 20:38 ./usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt
-rw-r--r-- root/root 451754 2015-12-21 20:38 ./usr/share/TVC/sse/motifset.txt
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/doc/tvc/
-rw-r--r-- root/root 1078 2021-10-31 14:47 ./usr/share/doc/tvc/README.Debian
-rw-r--r-- root/root 235 2021-10-31 15:00 ./usr/share/doc/tvc/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1240 2021-10-31 15:00 ./usr/share/doc/tvc/changelog.Debian.gz
-rw-r--r-- root/root 2939 2021-10-31 14:47 ./usr/share/doc/tvc/copyright
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/lintian/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 135 2021-10-31 14:47 ./usr/share/lintian/overrides/tvc
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 140496
Build-Time: 208
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 565
Job: tvc_5.0.3+git20151221.80e144e+dfsg-4
Machine Architecture: armhf
Package: tvc
Package-Time: 792
Source-Version: 5.0.3+git20151221.80e144e+dfsg-4
Space: 140496
Status: successful
Version: 5.0.3+git20151221.80e144e+dfsg-4+b1
--------------------------------------------------------------------------------
Finished at 2021-12-15T23:18:59Z
Build needed 00:13:12, 140496k disk space