tvc →
5.0.3+git20151221.80e144e+dfsg-5+b2 →
armhf → 2024-02-07 22:41:28
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+=================================================================================+
| tvc 5.0.3+git20151221.80e144e+dfsg-5+b2 (armhf) Wed, 07 Feb 2024 22:38:32 +0000 |
+=================================================================================+
Package: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-5+b2
Source Version: 5.0.3+git20151221.80e144e+dfsg-5
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-ea61e3cc-4544-4bf4-a4bc-ff6480dfe37b' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/tvc-L4M4hV/resolver-7xA6MV' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.4 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.1 MB]
Fetched 29.5 MB in 5s (5467 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: '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 757 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (dsc) [2227 B]
Get:2 http://172.17.4.1/private trixie-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (tar) [745 kB]
Get:3 http://172.17.4.1/private trixie-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (diff) [9800 B]
Fetched 757 kB in 0s (4681 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/tvc-L4M4hV/tvc-5.0.3+git20151221.80e144e+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/tvc-L4M4hV' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [716 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [748 B]
Fetched 2073 B in 0s (0 B/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarchive13 libarmadillo-dev libarmadillo12 libarpack2
libarpack2-dev libbamtools-dev libbamtools2.5.2 libblas-dev libblas3
libboost-math-dev libboost-math1.83-dev libboost-math1.83.0 libboost1.83-dev
libbrotli1 libcurl4 libcurl4-openssl-dev libdebhelper-perl libdisorder-dev
libdisorder0 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5
libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu72
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev libjsoncpp25
liblapack-dev liblapack3 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1
libproc2-0 libpsl5 librhash0 librtmp1 libsmithwaterman-dev libsmithwaterman0
libssh2-1 libssl-dev libsub-override-perl libsuperlu-dev libsuperlu6 libsz2
libtool libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps
sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format
elpa-cmake-mode ninja-build dh-make gettext-doc libasprintf-dev
libgettextpo-dev groff lrzip libitpp-dev libbamtools-doc liblapack-doc
libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev
libboost-container1.83-dev libboost-context1.83-dev
libboost-contract1.83-dev libboost-coroutine1.83-dev
libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev
libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev
libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev
libboost-locale1.83-dev libboost-log1.83-dev libboost-mpi-python1.83-dev
libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev
libboost-program-options1.83-dev libboost-python1.83-dev
libboost-random1.83-dev libboost-regex1.83-dev
libboost-serialization1.83-dev libboost-stacktrace1.83-dev
libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev
libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev
libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev
libcurl4-doc libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev
pkg-config libhdf5-doc libssl-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 publicsuffix
libltdl-dev libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarchive13 libarmadillo-dev libarmadillo12 libarpack2
libarpack2-dev libbamtools-dev libbamtools2.5.2 libblas-dev libblas3
libboost-math-dev libboost-math1.83-dev libboost-math1.83.0 libboost1.83-dev
libbrotli1 libcurl4 libcurl4-openssl-dev libdebhelper-perl libdisorder-dev
libdisorder0 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5
libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu72
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev libjsoncpp25
liblapack-dev liblapack3 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1
libproc2-0 libpsl5 librhash0 librtmp1 libsmithwaterman-dev libsmithwaterman0
libssh2-1 libssl-dev libsub-override-perl libsuperlu-dev libsuperlu6 libsz2
libtool libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps
sbuild-build-depends-main-dummy sensible-utils zlib1g-dev
0 upgraded, 85 newly installed, 0 to remove and 15 not upgraded.
Need to get 56.1 MB of archives.
After this operation, 347 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-6 [81.4 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-3 [1358 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libproc2-0 armhf 2:4.0.4-4 [54.8 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf procps armhf 2:4.0.4-4 [848 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libarchive13 armhf 3.7.2-1 [294 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.59.0-1 [61.9 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-4 [195 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libcurl4 armhf 8.5.0-2+rpi1 [377 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf libjsoncpp25 armhf 1.9.5-6 [64.7 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libuv1 armhf 1.46.0-3+rpi1 [129 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf cmake-data all 3.28.1-1 [2127 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf cmake armhf 3.28.1-1 [7787 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.13 [85.0 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.13 [889 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf hdf5-helpers armhf 1.10.10+repack-3 [23.2 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libaec0 armhf 1.1.2-1 [21.3 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libsz2 armhf 1.1.2-1 [7700 B]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libaec-dev armhf 1.1.2-1 [18.4 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 13.2.0-9+rpi1 [247 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libarpack2 armhf 3.9.1-1 [80.8 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libsuperlu6 armhf 6.0.1+dfsg1-1 [130 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libarmadillo12 armhf 1:12.6.7+dfsg-1 [99.5 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libblas-dev armhf 3.11.0-2 [106 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf liblapack-dev armhf 3.11.0-2 [3007 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libarpack2-dev armhf 3.9.1-1 [91.6 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libhdf5-103-1 armhf 1.10.10+repack-3 [1215 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libhdf5-fortran-102 armhf 1.10.10+repack-3 [77.3 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libhdf5-hl-100 armhf 1.10.10+repack-3 [59.9 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.10+repack-3 [34.1 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.10+repack-3 [112 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.10+repack-3 [20.5 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.3.dfsg-3 [903 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-2 [258 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf libjpeg-dev armhf 1:2.1.5-2 [71.8 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf libcurl4-openssl-dev armhf 8.5.0-2+rpi1 [461 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libssl-dev armhf 3.1.4-2 [2115 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libhdf5-dev armhf 1.10.10+repack-3 [2314 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf libsuperlu-dev armhf 6.0.1+dfsg1-1 [21.5 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf libarmadillo-dev armhf 1:12.6.7+dfsg-1 [408 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-5 [133 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libbamtools-dev armhf 2.5.2+dfsg-5 [185 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf libboost1.83-dev armhf 1.83.0-2 [10.6 MB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libboost-math1.83.0 armhf 1.83.0-2 [326 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libboost-math1.83-dev armhf 1.83.0-2 [344 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libboost-math-dev armhf 1.83.0.2 [3504 B]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-4 [4856 B]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-4 [4484 B]
Get:83 http://172.17.4.1/private trixie-staging/main armhf libjsoncpp-dev armhf 1.9.5-6 [24.5 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12 [32.4 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-12 [36.7 kB]
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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
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libproc2-0:armhf (2:4.0.4-4) ...
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Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
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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 (0.21-14) ...
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Setting up libtool (2.4.7-7) ...
Setting up libarchive13:armhf (3.7.2-1) ...
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Setting up libaec-dev:armhf (1.1.2-1) ...
Setting up libarpack2:armhf (3.9.1-1) ...
Setting up libjpeg-dev:armhf (1:2.1.5-2) ...
Setting up libsuperlu6:armhf (6.0.1+dfsg1-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
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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 dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
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Setting up libsuperlu-dev:armhf (6.0.1+dfsg1-1) ...
Setting up libarmadillo12 (1:12.6.7+dfsg-1) ...
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Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.12.0-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcurl4-openssl-dev:armhf (8.5.0-2+rpi1) ...
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Setting up libhdf5-cpp-103-1:armhf (1.10.10+repack-3) ...
Setting up cmake (3.28.1-1) ...
Setting up libhdf5-hl-100:armhf (1.10.10+repack-3) ...
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Setting up libhdf5-hl-cpp-100:armhf (1.10.10+repack-3) ...
Setting up libhdf5-fortran-102:armhf (1.10.10+repack-3) ...
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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 (1:12.6.7+dfsg-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-13+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.2+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 libc6-dev_2.37-13+rpi1 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 linux-libc-dev_6.5.6-1+rpi1+b1
Package versions: adduser_3.137 apt_2.7.9 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 cmake_3.28.1-1 cmake-data_3.28.1-1 coreutils_9.4-3 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-9+rpi1 dash_0.5.12-6 debconf_1.5.83 debhelper_13.13 debianutils_5.16 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.2+rpi1 dpkg-dev_1.22.2+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 gcc-13-base_13.2.0-9+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 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zlib1g_1:1.3.dfsg-3 zlib1g-dev_1:1.3.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: tvc
Binary: tvc
Architecture: any
Version: 5.0.3+git20151221.80e144e+dfsg-5
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Dominique Belhachemi <domibel@debian.org>, Andreas Tille <tille@debian.org>
Homepage: http://ioncommunity.thermofisher.com
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/tvc
Vcs-Git: https://salsa.debian.org/med-team/tvc.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev
Package-List:
tvc deb science optional arch=any
Checksums-Sha1:
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7d0306db9bc6dc0e7cd4dede9e0a4fc26451cb66 9800 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz
Checksums-Sha256:
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Files:
68b468ca5054fb3260ad9de40131b632 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz
57be1c85cdcb34a4bc11e0493cbe5570 9800 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz
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gpgv: Signature made Tue Sep 6 15:33:36 2022 UTC
gpgv: using RSA key 2D65BC1EB9665A6E97F9730AB3F5945285219E1F
gpgv: issuer "mdbilal@disroot.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc: no acceptable signature found
dpkg-source: info: extracting tvc in /<<PKGBUILDDIR>>
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-5.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-5+b2
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-ea61e3cc-4544-4bf4-a4bc-ff6480dfe37b
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package tvc
dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-5+b2
dpkg-buildpackage: info: source distribution trixie-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 && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf ..
CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- The C compiler identification is GNU 13.2.0
-- The CXX compiler identification is GNU 13.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- CMAKE_CXX_FLAGS: '-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2'
-- Configuring done (0.8s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_FIND_USE_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
dh_auto_build -a
cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend
make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend
make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/tvcassembly.dir/DependInfo.cmake "--color="
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/tvcutils.dir/DependInfo.cmake "--color="
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/tvc.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build
make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 6%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o
[ 6%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o
[ 6%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o
[ 6%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/IndelAssembly/IndelAssembly.cpp
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/VariantCaller.cpp
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/tvcutils/tvcutils.cpp
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/TargetsManager.cpp
[ 7%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/tvcutils/prepare_hotspots.cpp
[ 9%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/SampleManager.cpp
[ 10%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/BAMWalkerEngine.cpp
/<<PKGBUILDDIR>>/VariantCaller/VariantCaller.cpp: In function ‘void TheSilenceOfTheArmadillos(std::ofstream&)’:
/<<PKGBUILDDIR>>/VariantCaller/VariantCaller.cpp:36:24: warning: ‘void arma::set_stream_err1(const std::ostream&)’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
36 | arma::set_stream_err1(null_ostream);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/armadillo:404,
from /<<PKGBUILDDIR>>/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:83:1: note: declared here
83 | set_stream_err1(const std::ostream&)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/VariantCaller/VariantCaller.cpp:37:24: warning: ‘void arma::set_stream_err2(const std::ostream&)’ is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
37 | arma::set_stream_err2(null_ostream);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/armadillo_bits/debug.hpp:92:1: note: declared here
92 | set_stream_err2(const std::ostream&)
| ^~~~~~~~~~~~~~~
[ 12%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/Util/OptArgs.cpp
[ 14%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/tvcutils/validate_bed.cpp
[ 15%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/OrderedBAMWriter.cpp
In file included from /usr/include/c++/13/vector:72,
from /<<PKGBUILDDIR>>/Util/OptArgs.h:11,
from /<<PKGBUILDDIR>>/Util/OptArgs.cpp:4:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void OptArgs::StringToDoubleVector(std::vector<double>&, const std::string&, const std::string&, char)’ at /<<PKGBUILDDIR>>/Util/OptArgs.cpp:474:21:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 17%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/tvcutils/unify_vcf.cpp
[ 18%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/SampleManager.cpp
[ 20%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o -MF CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o.d -o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o -c /<<PKGBUILDDIR>>/Util/Utils.cpp
[ 21%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/TargetsManager.cpp
[ 23%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/IonVersion.cpp
[ 25%] 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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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
In file included from /<<PKGBUILDDIR>>/VariantCaller/tvcutils/viterbi.h:64,
from /<<PKGBUILDDIR>>/VariantCaller/tvcutils/unify_vcf.cpp:19:
/<<PKGBUILDDIR>>/VariantCaller/tvcutils/viterbi.hpp: In instantiation of ‘void markov_chain<T>::optimal_path() [with T = unsigned int]’:
/<<PKGBUILDDIR>>/VariantCaller/tvcutils/viterbi.hpp:64:3: required from ‘void markov_chain<T>::initialize(_ForwardIterator, _ForwardIterator, T, T) [with _ForwardIterator = __gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int> >; T = unsigned int]’
/<<PKGBUILDDIR>>/VariantCaller/tvcutils/viterbi.hpp:38:13: required from ‘markov_chain<T>::markov_chain(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int> >; T = unsigned int]’
/<<PKGBUILDDIR>>/VariantCaller/tvcutils/unify_vcf.cpp:550:69: required from here
/<<PKGBUILDDIR>>/VariantCaller/tvcutils/viterbi.hpp:114:13: warning: ignoring return value of ‘constexpr bool std::operator!=(const reverse_iterator<_Iterator>&, const reverse_iterator<_Iterator>&) [with _Iterator = __gnu_cxx::__normal_iterator<vector<long int>*, vector<vector<long int> > >]’, declared with attribute ‘nodiscard’ [-Wunused-result]
114 | for (; it != rend(), vit != values.rend(); it++, vit++) {
| ~~~^~~~~~~~~
In file included from /usr/include/c++/13/string:48,
from /<<PKGBUILDDIR>>/VariantCaller/tvcutils/unify_vcf.cpp:7:
/usr/include/c++/13/bits/stl_iterator.h:462:5: note: declared here
462 | operator!=(const reverse_iterator<_Iterator>& __x,
| ^~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 25%] Built target tvcassembly
[ 26%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/TargetsManager.cpp
[ 28%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/HandleVariant.cpp
[ 29%] Building CXX object CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/Util/OptArgs.cpp
[ 31%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/HotspotReader.cpp
In file included from /usr/include/c++/13/vector:72,
from /<<PKGBUILDDIR>>/Util/OptArgs.h:11,
from /<<PKGBUILDDIR>>/Util/OptArgs.cpp:4:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void OptArgs::StringToDoubleVector(std::vector<double>&, const std::string&, const std::string&, char)’ at /<<PKGBUILDDIR>>/Util/OptArgs.cpp:474:21:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from /<<PKGBUILDDIR>>/VariantCaller/tvcutils/unify_vcf.cpp:13:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator<markov_state>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<markov_state>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<markov_state*, std::vector<markov_state> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member 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>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = markov_state; _Alloc = std::allocator<markov_state>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void markov_chain<T>::generate_states(T, T) [with T = unsigned int]’ at /<<PKGBUILDDIR>>/VariantCaller/tvcutils/viterbi.hpp:78:21:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<markov_state*, std::vector<markov_state> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 32%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/external/vcflib/Variant.cpp
[ 34%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/external/vcflib/split.cpp
[ 35%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/MetricsManager.cpp
[ 37%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/external/vcflib/tabixpp/tabix.cpp
[ 39%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/MiscUtil.cpp
[ 40%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/ExtendParameters.cpp
[ 42%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/external/vcflib/tabixpp/index.c
/<<PKGBUILDDIR>>/external/vcflib/tabixpp/index.c: In function ‘ti_index_core’:
/<<PKGBUILDDIR>>/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;
| ^~~~~~~~
[ 43%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/external/vcflib/tabixpp/bgzf.c
/<<PKGBUILDDIR>>/external/vcflib/tabixpp/bgzf.c: In function ‘_bgzf_check_EOF’:
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 45%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/InputStructures.cpp
[ 46%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/VcfFormat.cpp
[ 48%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/Reads/ExtendedReadInfo.cpp
In file included from /usr/include/c++/13/map:62,
from /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/InputStructures.h:14,
from /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/InputStructures.cpp:7:
/usr/include/c++/13/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, LinearCalibrationModel>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, LinearCalibrationModel>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, LinearCalibrationModel> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, LinearCalibrationModel> >]’:
/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, LinearCalibrationModel>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, LinearCalibrationModel> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, LinearCalibrationModel> > >::const_iterator’ changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/InputStructures.h:12:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const DPTreephaser&}; _Tp = DPTreephaser; _Alloc = std::allocator<DPTreephaser>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<DPTreephaser>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = DPTreephaser; _Alloc = std::allocator<DPTreephaser>]’,
inlined from ‘PersistingThreadObjects::PersistingThreadObjects(const InputStructures&)’ at /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/InputStructures.cpp:323:38:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<DPTreephaser*, std::vector<DPTreephaser> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/map:63:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, LinearCalibrationModel>}; _Key = std::__cxx11::basic_string<char>; _Tp = LinearCalibrationModel; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, LinearCalibrationModel> >]’,
inlined from ‘std::__enable_if_t<std::is_constructible<std::pair<const _Key, _Tp>, _Pair>::value, std::pair<typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind<std::pair<const _Key, _Tp> >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair<std::__cxx11::basic_string<char>, LinearCalibrationModel>; _Key = std::__cxx11::basic_string<char>; _Tp = LinearCalibrationModel; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, LinearCalibrationModel> >]’ at /usr/include/c++/13/bits/stl_map.h:860:27,
inlined from ‘void RecalibrationHandler::ReadRecalibrationFromComments(const BamTools::SamHeader&, const std::map<std::__cxx11::basic_string<char>, int>&)’ at /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/InputStructures.cpp:272:36:
/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type ‘std::map<std::__cxx11::basic_string<char>, LinearCalibrationModel>::const_iterator’ {aka ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, LinearCalibrationModel>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, LinearCalibrationModel> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, LinearCalibrationModel> > >::const_iterator’} changed in GCC 7.1
640 | return _M_t._M_emplace_hint_unique(__pos,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
641 | std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 50%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/IonVersion.cpp
[ 51%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/Splice/ErrorMotifs.cpp
[ 53%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/Splice/LocalContext.cpp
[ 54%] Linking CXX executable tvcutils
/usr/bin/cmake -E cmake_link_script CMakeFiles/tvcutils.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -o tvcutils -lbamtools -lz -ljsoncpp -lsmithwaterman -ldisorder
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 54%] Built target tvcutils
[ 56%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/Splice/ClassifyVariant.cpp
[ 57%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/Splice/SpliceVariantHypotheses.cpp
[ 59%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o
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[ 60%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 /<<PKGBUILDDIR>>/VariantCaller/Filter/VariantAssist.cpp
/<<PKGBUILDDIR>>/VariantCaller/Filter/VariantAssist.cpp: In function ‘double VariantAssist::MannWhitneyU(std::vector<float>&, std::vector<float>&, bool)’:
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
/<<PKGBUILDDIR>>/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
[ 62%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o
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/<<PKGBUILDDIR>>/external/vcflib/tabixpp/index.c: In function ‘ti_index_core’:
/<<PKGBUILDDIR>>/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;
| ^~~~~~~~
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/<<PKGBUILDDIR>>/external/vcflib/tabixpp/bgzf.c: In function ‘_bgzf_check_EOF’:
/<<PKGBUILDDIR>>/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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
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[ 87%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -c /<<PKGBUILDDIR>>/BaseCaller/DPTreephaser.cpp
[ 89%] Building CXX object CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -MF CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o.d -o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -c /<<PKGBUILDDIR>>/Calibration/LinearCalibrationModel.cpp
[ 90%] Building CXX object CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o -MF CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o.d -o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o -c /<<PKGBUILDDIR>>/Calibration/FlowAlignment.cpp
[ 92%] Building CXX object CMakeFiles/tvc.dir/Util/OptArgs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvc.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o -c /<<PKGBUILDDIR>>/Util/OptArgs.cpp
[ 93%] Building CXX object CMakeFiles/tvc.dir/realignment/Realigner.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/realignment/Realigner.cpp.o -MF CMakeFiles/tvc.dir/realignment/Realigner.cpp.o.d -o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o -c /<<PKGBUILDDIR>>/realignment/Realigner.cpp
[ 95%] Building C object CMakeFiles/tvc.dir/file-io/ion_util.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/file-io/ion_util.c.o -MF CMakeFiles/tvc.dir/file-io/ion_util.c.o.d -o CMakeFiles/tvc.dir/file-io/ion_util.c.o -c /<<PKGBUILDDIR>>/file-io/ion_util.c
[ 96%] Building C object CMakeFiles/tvc.dir/file-io/ion_error.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/file-io/ion_error.c.o -MF CMakeFiles/tvc.dir/file-io/ion_error.c.o.d -o CMakeFiles/tvc.dir/file-io/ion_error.c.o -c /<<PKGBUILDDIR>>/file-io/ion_error.c
[ 98%] Building CXX object CMakeFiles/tvc.dir/IonVersion.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/IonVersion.cpp.o -MF CMakeFiles/tvc.dir/IonVersion.cpp.o.d -o CMakeFiles/tvc.dir/IonVersion.cpp.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/IonVersion.cpp
In file included from /usr/include/c++/13/vector:72,
from /<<PKGBUILDDIR>>/Util/OptArgs.h:11,
from /<<PKGBUILDDIR>>/Util/OptArgs.cpp:4:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘void OptArgs::StringToDoubleVector(std::vector<double>&, const std::string&, const std::string&, char)’ at /<<PKGBUILDDIR>>/Util/OptArgs.cpp:474:21:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[100%] Linking CXX executable tvc
/usr/bin/cmake -E cmake_link_script CMakeFiles/tvc.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o "CMakeFiles/tvc.dir/file-io/ion_util.c.o" "CMakeFiles/tvc.dir/file-io/ion_error.c.o" CMakeFiles/tvc.dir/IonVersion.cpp.o -o tvc -lbamtools -lz -lpthread -lblas -llapack -larmadillo -ljsoncpp -lsmithwaterman -ldisorder
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target tvc
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
dh_auto_test -a
cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=--verbose ARGS\+=-j4
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
Running tests...
/usr/bin/ctest --force-new-ctest-process --verbose -j4
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/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: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tvc
1: Working Directory: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
1: Test timeout computed to be: 10000000
test 2
Start 2: tvc_test_1_thread_sse_off
2: Test command: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tvc "--input-bam" "/<<PKGBUILDDIR>>/share/TVC/examples/example1/test.bam" "--reference" "/<<PKGBUILDDIR>>/share/TVC/examples/example1/reference.fasta" "--target-file" "/<<PKGBUILDDIR>>/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/<<PKGBUILDDIR>>/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test1" "--output-vcf" "small_variants.vcf"
2: Working Directory: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
2: Test timeout computed to be: 10000000
test 3
Start 3: tvc_test_4_threads_sse_off_with_parameter_file
3: Test command: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tvc "--input-bam" "/<<PKGBUILDDIR>>/share/TVC/examples/example1/test.bam" "--reference" "/<<PKGBUILDDIR>>/share/TVC/examples/example1/reference.fasta" "--target-file" "/<<PKGBUILDDIR>>/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/<<PKGBUILDDIR>>/share/TVC/sse/motifset.txt" "--parameters-file" "/<<PKGBUILDDIR>>/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/test2" "--output-vcf" "small_variants.vcf"
3: Working Directory: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
3: Test timeout computed to be: 10000000
test 4
Start 4: tvcutils_call
4: Test command: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tvcutils
4: Working Directory: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
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)
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!
2: TargetsManager: Loaded targets file /<<PKGBUILDDIR>>/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
1/8 Test #1: tvc_call ......................................... Passed 0.03 sec
test 5
Start 5: tvcutils_prepare_hotspots_call
5: Test command: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tvcutils "prepare_hotspots"
5: Working Directory: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
5: Test timeout computed to be: 10000000
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: 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!
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 /<<PKGBUILDDIR>>/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
3: Recalibration was detected from comment lines in bam file(s):
3: 1 unique blocks of recalibration info detected.
3: Loading systematic error contexts.
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:
2/8 Test #4: tvcutils_call .................................... Passed 0.04 sec
test 6
Start 6: tvcutils_validate_bed_call
6: Test command: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tvcutils "validate_bed"
6: Working Directory: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
6: Test timeout computed to be: 10000000
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: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tvcutils "unify_vcf"
7: Working Directory: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
7: 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:
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: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tvcassembly
8: Working Directory: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
8: Test timeout computed to be: 10000000
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 0.00 sec
2: Loaded.
3: Loaded.
2: Recalibration model: suppressed
2:
2:
2: [tvc] Normal termination. Processing time: 1 seconds.
3:
3:
3: [tvc] Normal termination. Processing time: 1 seconds.
7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 0.91 sec
8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 0.92 sec
100% tests passed, 0 tests failed out of 8
Total Test time (real) = 0.93 sec
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install --destdir=debian/tvc/ -a
cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<<BUILDDIR>>/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/bin/tvc
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/bin/tvcassembly
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/bin/tvcutils
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/bin/variant_caller_pipeline.py
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/pluginMedia
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/sse
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/sse/motifset.txt
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/expected
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/reference.dict
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/reference.fasta
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/test.bam
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/test.bed
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/test_original.bed
-- Installing: /<<PKGBUILDDIR>>/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed
make[1]: Leaving directory '/<<PKGBUILDDIR>>/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: package could avoid a useless dependency if debian/tvc/usr/bin/tvc debian/tvc/usr/bin/tvcutils 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/tvc debian/tvc/usr/bin/tvcassembly debian/tvc/usr/bin/tvcutils 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-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5+b2_armhf.deb'.
dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5+b2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../tvc_5.0.3+git20151221.80e144e+dfsg-5+b2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../tvc_5.0.3+git20151221.80e144e+dfsg-5+b2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2024-02-07T22:41:23Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
tvc_5.0.3+git20151221.80e144e+dfsg-5+b2_armhf.changes:
------------------------------------------------------
Format: 1.8
Date: Wed, 07 Feb 2024 22:39:43 +0000
Source: tvc (5.0.3+git20151221.80e144e+dfsg-5)
Binary: tvc tvc-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 5.0.3+git20151221.80e144e+dfsg-5+b2
Distribution: trixie-staging
Urgency: low
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Raspbian pi5 test autobuilder <root@raspbian.org>
Description:
tvc - genetic variant caller for Ion Torrent sequencing platforms
Changes:
tvc (5.0.3+git20151221.80e144e+dfsg-5+b2) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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Files:
7b441cbc5b3a04c05548dea07f18b276 11026320 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5+b2_armhf.deb
c3d5d6bdccf0249dd1665256207a1698 7816 science optional tvc_5.0.3+git20151221.80e144e+dfsg-5+b2_armhf.buildinfo
f7098b510ef4ba5ea40c279a72aaa4cc 945428 science optional tvc_5.0.3+git20151221.80e144e+dfsg-5+b2_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: tvc (5.0.3+git20151221.80e144e+dfsg-5)
Binary: tvc tvc-dbgsym
Architecture: armhf
Version: 5.0.3+git20151221.80e144e+dfsg-5+b2
Binary-Only-Changes:
tvc (5.0.3+git20151221.80e144e+dfsg-5+b2) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
.
-- Raspbian pi5 test autobuilder <root@raspbian.org> Wed, 07 Feb 2024 22:39:43 +0000
Checksums-Md5:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Wed, 07 Feb 2024 22:41:23 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-14),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.3),
bash (= 5.2.21-2),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.3-6),
bsdutils (= 1:2.39.3-6),
build-essential (= 12.10),
bzip2 (= 1.0.8-5+b2),
cmake (= 3.28.1-1),
cmake-data (= 3.28.1-1),
coreutils (= 9.4-3),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-13+rpi1),
cpp-13 (= 13.2.0-9+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.83),
debhelper (= 13.13),
debianutils (= 5.16),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
dpkg (= 1.22.2+rpi1),
dpkg-dev (= 1.22.2+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-9+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-13+rpi1),
gcc-12-base (= 12.3.0-13+rpi1),
gcc-13 (= 13.2.0-9+rpi1),
gcc-13-base (= 13.2.0-9+rpi1),
gettext (= 0.21-14),
gettext-base (= 0.21-14),
grep (= 3.11-4),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
hdf5-helpers (= 1.10.10+repack-3),
hostname (= 3.23+nmu2),
init-system-helpers (= 1.66),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-6),
libaec-dev (= 1.1.2-1),
libaec0 (= 1.1.2-1),
libarchive-zip-perl (= 1.68-1),
libarchive13 (= 3.7.2-1),
libarmadillo-dev (= 1:12.6.7+dfsg-1),
libarmadillo12 (= 1:12.6.7+dfsg-1),
libarpack2 (= 3.9.1-1),
libarpack2-dev (= 3.9.1-1),
libasan8 (= 13.2.0-9+rpi1),
libatomic1 (= 13.2.0-9+rpi1),
libattr1 (= 1:2.5.1-5),
libaudit-common (= 1:3.1.2-1),
libaudit1 (= 1:3.1.2-1),
libbamtools-dev (= 2.5.2+dfsg-5),
libbamtools2.5.2 (= 2.5.2+dfsg-5),
libbinutils (= 2.41-6+rpi1),
libblas-dev (= 3.11.0-2),
libblas3 (= 3.11.0-2),
libblkid1 (= 2.39.3-6),
libboost-math-dev (= 1.83.0.2),
libboost-math1.83-dev (= 1.83.0-2),
libboost-math1.83.0 (= 1.83.0-2),
libboost1.83-dev (= 1.83.0-2),
libbrotli1 (= 1.1.0-2),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.37-13+rpi1),
libc-dev-bin (= 2.37-13+rpi1),
libc6 (= 2.37-13+rpi1),
libc6-dev (= 2.37-13+rpi1),
libcap-ng0 (= 0.8.4-1),
libcap2 (= 1:2.66-4),
libcc1-0 (= 13.2.0-9+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-4),
libcrypt1 (= 1:4.4.36-4),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libcurl4 (= 8.5.0-2+rpi1),
libcurl4-openssl-dev (= 8.5.0-2+rpi1),
libdb5.3 (= 5.3.28+dfsg2-4),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.13),
libdisorder-dev (= 0.0.2+git20130809.8062ee1-4),
libdisorder0 (= 0.0.2+git20130809.8062ee1-4),
libdpkg-perl (= 1.22.2+rpi1),
libelf1 (= 0.188-2.1+rpi1),
libexpat1 (= 2.5.0-2),
libffi8 (= 3.4.4-2),
libfile-find-rule-perl (= 0.34-3),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libgcc-12-dev (= 12.3.0-13+rpi1),
libgcc-13-dev (= 13.2.0-9+rpi1),
libgcc-s1 (= 13.2.0-9+rpi1),
libgcrypt20 (= 1.10.3-2),
libgdbm-compat4 (= 1.23-5),
libgdbm6 (= 1.23-5),
libgfortran5 (= 13.2.0-9+rpi1),
libgmp10 (= 2:6.3.0+dfsg-2),
libgnutls30 (= 3.8.3-1),
libgomp1 (= 13.2.0-9+rpi1),
libgpg-error0 (= 1.47-3),
libgssapi-krb5-2 (= 1.20.1-5),
libhdf5-103-1 (= 1.10.10+repack-3),
libhdf5-cpp-103-1 (= 1.10.10+repack-3),
libhdf5-dev (= 1.10.10+repack-3),
libhdf5-fortran-102 (= 1.10.10+repack-3),
libhdf5-hl-100 (= 1.10.10+repack-3),
libhdf5-hl-cpp-100 (= 1.10.10+repack-3),
libhdf5-hl-fortran-100 (= 1.10.10+repack-3),
libhogweed6 (= 3.9.1-2),
libicu72 (= 72.1-4),
libidn2-0 (= 2.3.4-1),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libjpeg-dev (= 1:2.1.5-2),
libjpeg62-turbo (= 1:2.1.5-2),
libjpeg62-turbo-dev (= 1:2.1.5-2),
libjsoncpp-dev (= 1.9.5-6),
libjsoncpp25 (= 1.9.5-6),
libk5crypto3 (= 1.20.1-5),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-5),
libkrb5support0 (= 1.20.1-5),
liblapack-dev (= 3.11.0-2),
liblapack3 (= 3.11.0-2),
libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1+b1),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma5 (= 5.4.5-0.3),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmd0 (= 1.1.0-2),
libmount1 (= 2.39.3-6),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libncursesw6 (= 6.4+20240113-1),
libnettle8 (= 3.9.1-2),
libnghttp2-14 (= 1.59.0-1),
libnsl-dev (= 1.3.0-3),
libnsl2 (= 1.3.0-3),
libnumber-compare-perl (= 0.03-3),
libp11-kit0 (= 0.25.3-4),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpcre2-8-0 (= 10.42-4),
libperl5.38 (= 5.38.2-3),
libpipeline1 (= 1.5.7-1),
libproc2-0 (= 2:4.0.4-4),
libpsl5 (= 0.21.2-1+b1),
librhash0 (= 1.4.3-3),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg1-4),
libsasl2-modules-db (= 2.1.28+dfsg1-4),
libseccomp2 (= 2.5.4-2+rpi1),
libselinux1 (= 3.5-1),
libsframe1 (= 2.41-6+rpi1),
libsmartcols1 (= 2.39.3-6),
libsmithwaterman-dev (= 0.0+git20160702.2610e25-12),
libsmithwaterman0 (= 0.0+git20160702.2610e25-12),
libssh2-1 (= 1.11.0-4),
libssl-dev (= 3.1.4-2),
libssl3 (= 3.1.4-2),
libstdc++-13-dev (= 13.2.0-9+rpi1),
libstdc++6 (= 13.2.0-9+rpi1),
libsub-override-perl (= 0.10-1),
libsuperlu-dev (= 6.0.1+dfsg1-1),
libsuperlu6 (= 6.0.1+dfsg1-1),
libsystemd0 (= 254.5-1+rpi1),
libsz2 (= 1.1.2-1),
libtasn1-6 (= 4.19.0-3),
libtext-glob-perl (= 0.11-3),
libtinfo6 (= 6.4+20240113-1),
libtirpc-common (= 1.3.4+ds-1),
libtirpc-dev (= 1.3.4+ds-1),
libtirpc3 (= 1.3.4+ds-1),
libtool (= 2.4.7-7),
libubsan1 (= 13.2.0-9+rpi1),
libuchardet0 (= 0.0.8-1),
libudev1 (= 254.5-1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.3-6),
libuv1 (= 1.46.0-3+rpi1),
libxml2 (= 2.9.14+dfsg-1.3),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1+b1),
login (= 1:4.13+dfsg1-3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.0-3),
mawk (= 1.3.4.20231126-1),
ncurses-base (= 6.4+20240113-1),
ncurses-bin (= 6.4+20240113-1),
patch (= 2.7.6-7),
perl (= 5.38.2-3),
perl-base (= 5.38.2-3),
perl-modules-5.38 (= 5.38.2-3),
po-debconf (= 1.0.21+nmu1),
procps (= 2:4.0.4-4),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-2),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-5),
tar (= 1.35+dfsg-3),
usr-is-merged (= 38),
usrmerge (= 38),
util-linux (= 2.39.3-6),
xz-utils (= 5.4.5-0.3),
zlib1g (= 1:1.3.dfsg-3),
zlib1g-dev (= 1:1.3.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1707345583"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5+b2_armhf.deb
--------------------------------------------------------
new Debian package, version 2.0.
size 11026320 bytes: control archive=724 bytes.
529 bytes, 12 lines control
401 bytes, 4 lines md5sums
Package: tvc-dbgsym
Source: tvc (5.0.3+git20151221.80e144e+dfsg-5)
Version: 5.0.3+git20151221.80e144e+dfsg-5+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 11070
Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-5+b2)
Section: debug
Priority: optional
Description: debug symbols for tvc
Build-Ids: 0c08474c140a14b28167ecc4b8b5de710239dedb 906c5140bb5547d857c2502e09d03dd5511126d2 e1c1047fac1a67e6782b332e5390c46564d57d04
drwxr-xr-x root/root 0 2024-02-07 22:39 ./
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/lib/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/lib/debug/.build-id/0c/
-rw-r--r-- root/root 2206732 2024-02-07 22:39 ./usr/lib/debug/.build-id/0c/08474c140a14b28167ecc4b8b5de710239dedb.debug
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/lib/debug/.build-id/90/
-rw-r--r-- root/root 7823324 2024-02-07 22:39 ./usr/lib/debug/.build-id/90/6c5140bb5547d857c2502e09d03dd5511126d2.debug
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/lib/debug/.build-id/e1/
-rw-r--r-- root/root 814300 2024-02-07 22:39 ./usr/lib/debug/.build-id/e1/c1047fac1a67e6782b332e5390c46564d57d04.debug
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 474844 2024-02-07 22:39 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/tvc.debug
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/share/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-02-07 22:39 ./usr/share/doc/tvc-dbgsym -> tvc
tvc_5.0.3+git20151221.80e144e+dfsg-5+b2_armhf.deb
-------------------------------------------------
new Debian package, version 2.0.
size 945428 bytes: control archive=1724 bytes.
1046 bytes, 17 lines control
2537 bytes, 29 lines md5sums
Package: tvc
Source: tvc (5.0.3+git20151221.80e144e+dfsg-5)
Version: 5.0.3+git20151221.80e144e+dfsg-5+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3008
Depends: libarmadillo12 (>= 1:12.6.7+dfsg), libbamtools2.5.2 (>= 2.5.2+dfsg), libc6 (>= 2.34), libdisorder0 (>= 0.0.2), libgcc-s1 (>= 3.5), libjsoncpp25 (>= 1.9.5), libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 13.1), 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 2024-02-07 22:39 ./
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/bin/
-rwxr-xr-x root/root 954336 2024-02-07 22:39 ./usr/bin/tvc
-rwxr-xr-x root/root 182564 2024-02-07 22:39 ./usr/bin/tvcassembly
-rwxr-xr-x root/root 494136 2024-02-07 22:39 ./usr/bin/tvcutils
-rwxr-xr-x root/root 12985 2024-02-07 22:39 ./usr/bin/variant_caller_pipeline.py
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/share/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/share/TVC/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/share/TVC/examples/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/share/TVC/examples/example1/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./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 2024-02-07 22:39 ./usr/share/TVC/pluginMedia/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./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 2024-02-07 22:39 ./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 2024-02-07 22:39 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/share/doc/tvc/
-rw-r--r-- root/root 1078 2022-09-05 16:49 ./usr/share/doc/tvc/README.Debian
-rw-r--r-- root/root 232 2024-02-07 22:39 ./usr/share/doc/tvc/changelog.Debian.armhf.gz
-rw-r--r-- root/root 657 2024-02-07 22:39 ./usr/share/doc/tvc/changelog.Debian.gz
-rw-r--r-- root/root 2939 2022-09-05 17:19 ./usr/share/doc/tvc/copyright
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/share/lintian/
drwxr-xr-x root/root 0 2024-02-07 22:39 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 135 2022-09-05 16:49 ./usr/share/lintian/overrides/tvc
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 138348
Build-Time: 100
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 62
Job: tvc_5.0.3+git20151221.80e144e+dfsg-5
Machine Architecture: arm64
Package: tvc
Package-Time: 171
Source-Version: 5.0.3+git20151221.80e144e+dfsg-5
Space: 138348
Status: successful
Version: 5.0.3+git20151221.80e144e+dfsg-5+b2
--------------------------------------------------------------------------------
Finished at 2024-02-07T22:41:23Z
Build needed 00:02:51, 138348k disk space