Raspbian Package Auto-Building

Build log for tvc (5.0.3+git20151221.80e144e+dfsg-4+b3) on armhf

tvc → 5.0.3+git20151221.80e144e+dfsg-4+b3 → armhf → 2022-09-05 17:10:29 

sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019

+=================================================================================+
| tvc 5.0.3+git20151221.80e144e+dfsg-4+b3 (armhf) Mon, 05 Sep 2022 16:46:46 +0000 |
+=================================================================================+

Package: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-4+b3
Source Version: 5.0.3+git20151221.80e144e+dfsg-4
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-ef2a5c81-959f-427e-b3ea-991dde2bb746' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/tvc-UvaTiC/resolver-Z6Pvjj' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.2 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.1 MB]
Fetched 27.4 MB in 18s (1522 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-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 756 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-4 (dsc) [2200 B]
Get:2 http://172.17.4.1/private bookworm-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-4 (tar) [745 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-4 (diff) [9248 B]
Fetched 756 kB in 0s (3461 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/tvc-UvaTiC/tvc-5.0.3+git20151221.80e144e+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/tvc-UvaTiC' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 12), 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 [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [417 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [500 B]
Fetched 1874 B in 0s (26.4 kB/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 packages were automatically installed and are no longer required:
  krb5-locales libpam-cap
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
  cpp-12 debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism
  dmsetup dwz emacsen-common file g++-12 gcc-12 gcc-12-base gettext
  gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
  libapparmor1 libarchive-zip-perl libarchive13 libargon2-1 libarmadillo-dev
  libarmadillo11 libarpack2 libarpack2-dev libasan8 libatomic1 libbamtools-dev
  libbamtools2.5.2 libblas-dev libblas3 libboost-math-dev
  libboost-math1.74-dev libboost-math1.74.0 libboost1.74-dev libbrotli1
  libcc1-0 libcryptsetup12 libcurl4 libcurl4-openssl-dev libdebhelper-perl
  libdevmapper1.02.1 libdisorder-dev libdisorder0 libelf1 libexpat1 libfdisk1
  libfile-stripnondeterminism-perl libgcc-12-dev libgcc-s1 libgfortran5
  libgomp1 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
  libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu71 libip4tc2
  libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjson-c5 libjsoncpp-dev
  libjsoncpp25 libkmod2 liblapack-dev liblapack3 libmagic-mgc libmagic1
  libncurses6 libnghttp2-14 libpipeline1 libprocps8 libpsl5 librhash0 librtmp1
  libsmithwaterman-dev libsmithwaterman0 libssh2-1 libssl-dev libstdc++-12-dev
  libstdc++6 libsub-override-perl libsuperlu-dev libsuperlu5 libsystemd-shared
  libsz2 libtool libubsan1 libuchardet0 libuv1 libxml2 m4 man-db po-debconf
  procps systemd zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build
  cmake-format gcc-12-locales dh-make gcc-12-doc gettext-doc libasprintf-dev
  libgettextpo-dev groff lrzip libitpp-dev libbamtools-doc liblapack-doc
  libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev
  libboost-container1.74-dev libboost-context1.74-dev
  libboost-contract1.74-dev libboost-coroutine1.74-dev
  libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
  libboost-filesystem1.74-dev libboost-graph1.74-dev
  libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
  libboost-locale1.74-dev libboost-log1.74-dev libboost-mpi1.74-dev
  libboost-mpi-python1.74-dev libboost-numpy1.74-dev
  libboost-program-options1.74-dev libboost-python1.74-dev
  libboost-random1.74-dev libboost-regex1.74-dev
  libboost-serialization1.74-dev libboost-stacktrace1.74-dev
  libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
  libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
  libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
  libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev
  pkg-config libhdf5-doc libssl-doc libstdc++-12-doc libsuperlu-doc
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
  www-browser libmail-box-perl systemd-container systemd-homed systemd-userdbd
  systemd-boot libfido2-1 libtss2-esys-3.0.2-0 libtss2-mu0 libtss2-rc0
  policykit-1
Recommended packages:
  curl | wget | lynx ca-certificates libarchive-cpio-perl libgpm2 publicsuffix
  libltdl-dev libmail-sendmail-perl psmisc default-dbus-system-bus
  | dbus-system-bus systemd-timesyncd | time-daemon
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
  debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dmsetup dwz
  emacsen-common file gettext gettext-base groff-base hdf5-helpers
  intltool-debian libaec-dev libaec0 libapparmor1 libarchive-zip-perl
  libarchive13 libargon2-1 libarmadillo-dev libarmadillo11 libarpack2
  libarpack2-dev libbamtools-dev libbamtools2.5.2 libblas-dev libblas3
  libboost-math-dev libboost-math1.74-dev libboost-math1.74.0 libboost1.74-dev
  libbrotli1 libcryptsetup12 libcurl4 libcurl4-openssl-dev libdebhelper-perl
  libdevmapper1.02.1 libdisorder-dev libdisorder0 libelf1 libexpat1 libfdisk1
  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 libicu71 libip4tc2 libjpeg-dev
  libjpeg62-turbo libjpeg62-turbo-dev libjson-c5 libjsoncpp-dev libjsoncpp25
  libkmod2 liblapack-dev liblapack3 libmagic-mgc libmagic1 libncurses6
  libnghttp2-14 libpipeline1 libprocps8 libpsl5 librhash0 librtmp1
  libsmithwaterman-dev libsmithwaterman0 libssh2-1 libssl-dev
  libsub-override-perl libsuperlu-dev libsuperlu5 libsystemd-shared libsz2
  libtool libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps
  sbuild-build-depends-main-dummy systemd zlib1g-dev
The following packages will be upgraded:
  cpp-12 g++-12 gcc-12 gcc-12-base libasan8 libatomic1 libcc1-0 libgcc-12-dev
  libgcc-s1 libgomp1 libstdc++-12-dev libstdc++6 libubsan1
13 upgraded, 98 newly installed, 0 to remove and 7 not upgraded.
Need to get 222 MB of archives.
After this operation, 339 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 bookworm-staging/main armhf libargon2-1 armhf 0~20171227-0.3 [19.6 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf dmsetup armhf 2:1.02.185-1 [91.8 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libdevmapper1.02.1 armhf 2:1.02.185-1 [134 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libjson-c5 armhf 0.16-1 [40.0 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libcryptsetup12 armhf 2:2.5.0-2 [225 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libfdisk1 armhf 2.38.1-1 [237 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libkmod2 armhf 30+20220630-3 [51.8 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libapparmor1 armhf 3.0.7-1 [98.9 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libip4tc2 armhf 1.8.8-1 [32.9 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libsystemd-shared armhf 251.3-1+rpi1 [1526 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf systemd armhf 251.3-1+rpi1 [2985 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libubsan1 armhf 12.1.0-8+rpi1 [861 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf gcc-12-base armhf 12.1.0-8+rpi1 [208 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libstdc++6 armhf 12.1.0-8+rpi1 [505 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libgomp1 armhf 12.1.0-8+rpi1 [95.9 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libatomic1 armhf 12.1.0-8+rpi1 [8236 B]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libasan8 armhf 12.1.0-8+rpi1 [2090 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf cpp-12 armhf 12.1.0-8+rpi1 [50.1 MB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libcc1-0 armhf 12.1.0-8+rpi1 [32.2 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf g++-12 armhf 12.1.0-8+rpi1 [54.0 MB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf gcc-12 armhf 12.1.0-8+rpi1 [55.9 MB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libgcc-12-dev armhf 12.1.0-8+rpi1 [725 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-12-dev armhf 12.1.0-8+rpi1 [2026 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libgcc-s1 armhf 12.1.0-8+rpi1 [36.2 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1 [137 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-2 [34.2 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-2 [1364 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-7 [60.7 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-7 [475 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-8 [171 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-8 [510 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libarchive13 armhf 3.6.0-1 [306 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.49.0-1 [69.8 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.84.0-2 [321 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.8-1 [84.1 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp25 armhf 1.9.5-4 [66.7 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libuv1 armhf 1.44.1-2+rpi1 [124 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf dh-elpa-helper all 2.0.10 [11.3 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf emacsen-common all 3.0.4 [19.3 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf cmake-data all 3.24.1-1 [2018 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf cmake armhf 3.24.1-1 [3654 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.9.1 [196 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-3 [10.4 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-1 [175 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-8 [1219 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.9.1 [1071 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf hdf5-helpers armhf 1.10.7+repack-4+rpi1+b1 [43.2 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libaec0 armhf 1.0.6-1 [19.3 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libsz2 armhf 1.0.6-1 [7452 B]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libaec-dev armhf 1.0.6-1 [17.6 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.1.0-8+rpi1 [238 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libarpack2 armhf 3.8.0-1 [85.9 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libsuperlu5 armhf 5.3.0+dfsg1-2 [128 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libarmadillo11 armhf 1:11.2.3+dfsg-1 [100.0 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.1-2 [114 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.1-2 [2847 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libarpack2-dev armhf 3.8.0-1 [94.6 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-103-1 armhf 1.10.7+repack-4+rpi1+b1 [1240 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-fortran-102 armhf 1.10.7+repack-4+rpi1+b1 [97.4 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-100 armhf 1.10.7+repack-4+rpi1+b1 [82.4 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.7+repack-4+rpi1+b1 [54.2 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.7+repack-4+rpi1+b1 [132 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.7+repack-4+rpi1+b1 [40.3 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.2-1 [261 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.1.2-1 [74.7 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-openssl-dev armhf 7.84.0-2 [397 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 3.0.5-2 [2116 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-dev armhf 1.10.7+repack-4+rpi1+b1 [2208 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libsuperlu-dev armhf 5.3.0+dfsg1-2 [22.1 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libarmadillo-dev armhf 1:11.2.3+dfsg-1 [404 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-2 [127 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libbamtools-dev armhf 2.5.2+dfsg-2 [183 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-17 [9534 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libboost-math1.74.0 armhf 1.74.0-17 [346 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libboost-math1.74-dev armhf 1.74.0-17 [402 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libboost-math-dev armhf 1.74.0.3+b4 [4808 B]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-4 [4856 B]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-4 [4484 B]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp-dev armhf 1.9.5-4 [26.4 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12 [32.4 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-12 [36.7 kB]
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Unpacking libdisorder0:armhf (0.0.2+git20130809.8062ee1-4) ...
Selecting previously unselected package libdisorder-dev:armhf.
Preparing to unpack .../82-libdisorder-dev_0.0.2+git20130809.8062ee1-4_armhf.deb ...
Unpacking libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-4) ...
Selecting previously unselected package libjsoncpp-dev:armhf.
Preparing to unpack .../83-libjsoncpp-dev_1.9.5-4_armhf.deb ...
Unpacking libjsoncpp-dev:armhf (1.9.5-4) ...
Selecting previously unselected package libsmithwaterman0:armhf.
Preparing to unpack .../84-libsmithwaterman0_0.0+git20160702.2610e25-12_armhf.deb ...
Unpacking libsmithwaterman0:armhf (0.0+git20160702.2610e25-12) ...
Selecting previously unselected package libsmithwaterman-dev:armhf.
Preparing to unpack .../85-libsmithwaterman-dev_0.0+git20160702.2610e25-12_armhf.deb ...
Unpacking libsmithwaterman-dev:armhf (0.0+git20160702.2610e25-12) ...
Selecting previously unselected package sbuild-build-depends-main-dummy.
Preparing to unpack .../86-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libip4tc2:armhf (1.8.8-1) ...
Setting up libexpat1:armhf (2.4.8-1) ...
Setting up libpipeline1:armhf (1.5.6-2) ...
Setting up libdisorder0:armhf (0.0.2+git20130809.8062ee1-4) ...
Setting up libicu71:armhf (71.1-3) ...
Setting up libapparmor1:armhf (3.0.7-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up cpp-12 (12.1.0-8+rpi1) ...
Setting up bsdextrautils (2.38.1-1) ...
Setting up hdf5-helpers (1.10.7+repack-4+rpi1+b1) ...
Setting up libmagic-mgc (1:5.41-4) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libargon2-1:armhf (0~20171227-0.3) ...
Setting up libdebhelper-perl (13.9.1) ...
Setting up libbrotli1:armhf (1.0.9-2+b2) ...
Setting up libsmithwaterman0:armhf (0.0+git20160702.2610e25-12) ...
Setting up libnghttp2-14:armhf (1.49.0-1) ...
Setting up libmagic1:armhf (1:5.41-4) ...
Setting up gettext-base (0.21-8) ...
Setting up m4 (1.4.19-1) ...
Setting up file (1:5.41-4) ...
Setting up libgomp1:armhf (12.1.0-8+rpi1) ...
Setting up libaec0:armhf (1.0.6-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libuv1:armhf (1.44.1-2+rpi1) ...
Setting up libjpeg62-turbo:armhf (1:2.1.2-1) ...
Setting up emacsen-common (3.0.4) ...
Setting up libjpeg62-turbo-dev:armhf (1:2.1.2-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up dh-elpa-helper (2.0.10) ...
Setting up libncurses6:armhf (6.3+20220423-2) ...
Setting up libssl-dev:armhf (3.0.5-2) ...
Setting up libatomic1:armhf (12.1.0-8+rpi1) ...
Setting up autopoint (0.21-8) ...
Setting up libjsoncpp25:armhf (1.9.5-4) ...
Setting up libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-4) ...
Setting up libbamtools2.5.2:armhf (2.5.2+dfsg-2) ...
Setting up libgfortran5:armhf (12.1.0-8+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up libfdisk1:armhf (2.38.1-1) ...
Setting up libboost-math1.74.0:armhf (1.74.0-17) ...
Setting up libubsan1:armhf (12.1.0-8+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-4.1) ...
Setting up librhash0:armhf (1.4.3-3) ...
Setting up libasan8:armhf (12.1.0-8+rpi1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-3) ...
Setting up libssh2-1:armhf (1.10.0-3+b1) ...
Setting up cmake-data (3.24.1-1) ...
Setting up libelf1:armhf (0.187-1) ...
Setting up libjson-c5:armhf (0.16-1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1) ...
Setting up libcc1-0:armhf (12.1.0-8+rpi1) ...
Setting up libprocps8:armhf (2:3.3.17-7) ...
Setting up libblas-dev:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libsz2:armhf (1.0.6-1) ...
Setting up libkmod2:armhf (30+20220630-3) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up libjsoncpp-dev:armhf (1.9.5-4) ...
Setting up liblapack3:armhf (3.10.1-2) ...
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 (0.21-8) ...
Setting up libtool (2.4.7-4) ...
Setting up libarchive13:armhf (3.6.0-1) ...
Setting up libaec-dev:armhf (1.0.6-1) ...
Setting up libarpack2:armhf (3.8.0-1) ...
Setting up libjpeg-dev:armhf (1:2.1.2-1) ...
Setting up libsuperlu5:armhf (5.3.0+dfsg1-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up dh-autoreconf (20) ...
Setting up libbamtools-dev:armhf (2.5.2+dfsg-2) ...
Setting up libgcc-12-dev:armhf (12.1.0-8+rpi1) ...
Setting up liblapack-dev:armhf (3.10.1-2) ...
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 libsystemd-shared:armhf (251.3-1+rpi1) ...
Setting up libsmithwaterman-dev:armhf (0.0+git20160702.2610e25-12) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-8) ...
Setting up procps (2:3.3.17-7) ...
Setting up libcurl4:armhf (7.84.0-2) ...
Setting up libsuperlu-dev:armhf (5.3.0+dfsg1-2) ...
Setting up libarpack2-dev:armhf (3.8.0-1) ...
Setting up libarmadillo11 (1:11.2.3+dfsg-1) ...
Setting up libstdc++-12-dev:armhf (12.1.0-8+rpi1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up gcc-12 (12.1.0-8+rpi1) ...
Setting up libcurl4-openssl-dev:armhf (7.84.0-2) ...
Setting up libhdf5-103-1:armhf (1.10.7+repack-4+rpi1+b1) ...
Setting up libhdf5-cpp-103-1:armhf (1.10.7+repack-4+rpi1+b1) ...
Setting up cmake (3.24.1-1) ...
Setting up libhdf5-hl-100:armhf (1.10.7+repack-4+rpi1+b1) ...
Setting up g++-12 (12.1.0-8+rpi1) ...
Setting up libboost1.74-dev:armhf (1.74.0-17) ...
Setting up libhdf5-hl-cpp-100:armhf (1.10.7+repack-4+rpi1+b1) ...
Setting up libhdf5-fortran-102:armhf (1.10.7+repack-4+rpi1+b1) ...
Setting up libhdf5-hl-fortran-100:armhf (1.10.7+repack-4+rpi1+b1) ...
Setting up libboost-math1.74-dev:armhf (1.74.0-17) ...
Setting up libboost-math-dev:armhf (1.74.0.3+b4) ...
Setting up libhdf5-dev (1.10.7+repack-4+rpi1+b1) ...
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 (1:11.2.3+dfsg-1) ...
Setting up libdevmapper1.02.1:armhf (2:1.02.185-1) ...
Setting up dmsetup (2:1.02.185-1) ...
Setting up libcryptsetup12:armhf (2:2.5.0-2) ...
Setting up systemd (251.3-1+rpi1) ...
Created symlink /etc/systemd/system/getty.target.wants/getty@tty1.service → /lib/systemd/system/getty@.service.
Created symlink /etc/systemd/system/multi-user.target.wants/remote-fs.target → /lib/systemd/system/remote-fs.target.
Created symlink /etc/systemd/system/sysinit.target.wants/systemd-pstore.service → /lib/systemd/system/systemd-pstore.service.
Initializing machine ID from random generator.
Setting up man-db (2.10.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer.
Setting up debhelper (13.9.1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.33-8+rpi1) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.38.90.20220713-2+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.1.0-8+rpi1 gcc-12_12.1.0-8+rpi1 libc6-dev_2.33-8+rpi1 libstdc++-12-dev_12.1.0-8+rpi1 libstdc++6_12.1.0-8+rpi1 linux-libc-dev_5.18.14-1+rpi1
Package versions: adduser_3.123 apt_2.5.2 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-8 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.6.0 bash_5.1-6.1 binutils_2.38.90.20220713-2+rpi1 binutils-arm-linux-gnueabihf_2.38.90.20220713-2+rpi1 binutils-common_2.38.90.20220713-2+rpi1 bsdextrautils_2.38.1-1 bsdutils_1:2.38.1-1 build-essential_12.9 bzip2_1.0.8-5+b2 cmake_3.24.1-1 cmake-data_3.24.1-1 coreutils_8.32-4.1 cpp_4:12.1.0-3+rpi1 cpp-12_12.1.0-8+rpi1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.9.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-elpa-helper_2.0.10 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.35-3 dmsetup_2:1.02.185-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 emacsen-common_3.0.4 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.1.0-3+rpi1 g++-12_12.1.0-8+rpi1 gcc_4:12.1.0-3+rpi1 gcc-12_12.1.0-8+rpi1 gcc-12-base_12.1.0-8+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-8 gettext-base_0.21-8 gnupg_2.2.35-3 gnupg-l10n_2.2.35-3 gnupg-utils_2.2.35-3 gpg_2.2.35-3 gpg-agent_2.2.35-3 gpg-wks-client_2.2.35-3 gpg-wks-server_2.2.35-3 gpgconf_2.2.35-3 gpgsm_2.2.35-3 gpgv_2.2.35-3 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hdf5-helpers_1.10.7+repack-4+rpi1+b1 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapparmor1_3.0.7-1 libapt-pkg6.0_2.5.2 libarchive-zip-perl_1.68-1 libarchive13_3.6.0-1 libargon2-1_0~20171227-0.3 libarmadillo-dev_1:11.2.3+dfsg-1 libarmadillo11_1:11.2.3+dfsg-1 libarpack2_3.8.0-1 libarpack2-dev_3.8.0-1 libasan8_12.1.0-8+rpi1 libassuan0_2.5.5-4 libatomic1_12.1.0-8+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbamtools-dev_2.5.2+dfsg-2 libbamtools2.5.2_2.5.2+dfsg-2 libbinutils_2.38.90.20220713-2+rpi1 libblas-dev_3.10.1-2 libblas3_3.10.1-2 libblkid1_2.38.1-1 libboost-math-dev_1.74.0.3+b4 libboost-math1.74-dev_1.74.0-17 libboost-math1.74.0_1.74.0-17 libboost1.74-dev_1.74.0-17 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.33-8+rpi1 libc-dev-bin_2.33-8+rpi1 libc6_2.33-8+rpi1 libc6-dev_2.33-8+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.1.0-8+rpi1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libcryptsetup12_2:2.5.0-2 libctf-nobfd0_2.38.90.20220713-2+rpi1 libctf0_2.38.90.20220713-2+rpi1 libcurl4_7.84.0-2 libcurl4-openssl-dev_7.84.0-2 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.263 libdebhelper-perl_13.9.1 libdevmapper1.02.1_2:1.02.185-1 libdisorder-dev_0.0.2+git20130809.8062ee1-4 libdisorder0_0.0.2+git20130809.8062ee1-4 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-1 libexpat1_2.4.8-1 libext2fs2_1.46.5-2 libfakeroot_1.29-1 libfdisk1_2.38.1-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.1.0-8+rpi1 libgcc-s1_12.1.0-8+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgfortran5_12.1.0-8+rpi1 libgmp10_2:6.2.1+dfsg1-1 libgnutls30_3.7.7-2 libgomp1_12.1.0-8+rpi1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.20-1 libhdf5-103-1_1.10.7+repack-4+rpi1+b1 libhdf5-cpp-103-1_1.10.7+repack-4+rpi1+b1 libhdf5-dev_1.10.7+repack-4+rpi1+b1 libhdf5-fortran-102_1.10.7+repack-4+rpi1+b1 libhdf5-hl-100_1.10.7+repack-4+rpi1+b1 libhdf5-hl-cpp-100_1.10.7+repack-4+rpi1+b1 libhdf5-hl-fortran-100_1.10.7+repack-4+rpi1+b1 libhogweed6_3.8.1-2 libicu71_71.1-3 libidn2-0_2.3.3-1 libip4tc2_1.8.8-1 libisl23_0.25-1 libjpeg-dev_1:2.1.2-1 libjpeg62-turbo_1:2.1.2-1 libjpeg62-turbo-dev_1:2.1.2-1 libjson-c5_0.16-1 libjsoncpp-dev_1.9.5-4 libjsoncpp25_1.9.5-4 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkmod2_30+20220630-3 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 liblapack-dev_3.10.1-2 liblapack3_3.10.1-2 libldap-2.5-0_2.5.12+dfsg-2 liblz4-1_1.9.3-2 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38.1-1 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.49.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-2 libpam-modules-bin_1.5.2-2 libpam-runtime_1.5.2-2 libpam0g_1.5.2-2 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.32_5.32.1-6 libperl5.34_5.34.0-5 libpipeline1_1.5.6-2 libprocps8_2:3.3.17-7 libpsl5_0.21.0-1.2 libreadline8_8.1.2-1.2 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-7 libsasl2-modules-db_2.1.28+dfsg-7 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-1 libsmithwaterman-dev_0.0+git20160702.2610e25-12 libsmithwaterman0_0.0+git20160702.2610e25-12 libsqlite3-0_3.39.2-1 libss2_1.46.5-2 libssh2-1_1.10.0-3+b1 libssl-dev_3.0.5-2 libssl1.1_1.1.1o-1 libssl3_3.0.5-2 libstdc++-12-dev_12.1.0-8+rpi1 libstdc++6_12.1.0-8+rpi1 libsub-override-perl_0.09-3 libsuperlu-dev_5.3.0+dfsg1-2 libsuperlu5_5.3.0+dfsg1-2 libsystemd-shared_251.3-1+rpi1 libsystemd0_251.3-1+rpi1 libsz2_1.0.6-1 libtasn1-6_4.18.0-4 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.1.0-8+rpi1 libuchardet0_0.0.7-1 libudev1_251.3-1+rpi1 libunistring2_1.0-1 libuuid1_2.38.1-1 libuv1_1.44.1-2+rpi1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.18.14-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.2+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.10.2-2 mawk_1.3.4.20200120-3.1 mount_2.38.1-1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-5 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 procps_2:3.3.17-7 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 systemd_251.3-1+rpi1 sysvinit-utils_3.04-1 tar_1.34+dfsg-1 tzdata_2022c-1 util-linux_2.38.1-1 util-linux-extra_2.38.1-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1

+------------------------------------------------------------------------------+
| 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-4
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: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/tvc
Vcs-Git: https://salsa.debian.org/med-team/tvc.git
Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev
Package-List:
 tvc deb science optional arch=any
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 cd0223b1b1c96a2cc5a25fbc64e4e36a00347788 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz
 6f76b58c0913d4ad218ced30c803dbd5137c6b94 9248 tvc_5.0.3+git20151221.80e144e+dfsg-4.debian.tar.xz
Checksums-Sha256:
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Files:
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.arjLYpxw/trustedkeys.kbx': General error
gpgv: Signature made Sun Oct 31 15:09:13 2021 UTC
gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv:                issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./tvc_5.0.3+git20151221.80e144e+dfsg-4.dsc
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-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying cmake.patch
dpkg-source: info: applying bamtools.patch
dpkg-source: info: applying help.patch
dpkg-source: info: applying hurd.patch
dpkg-source: info: applying sse.patch
dpkg-source: info: applying use_debian_packaged_smithwaterman.patch
dpkg-source: info: applying python3.patch
dpkg-source: info: applying gcc11.patch

Check disk space
----------------

Sufficient free space for build

Hack binNMU version
-------------------

Created changelog entry for binNMU version 5.0.3+git20151221.80e144e+dfsg-4+b3

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=d1c922bed77e43309a96ad86c8684399
JOURNAL_STREAM=8:28455
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
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-ef2a5c81-959f-427e-b3ea-991dde2bb746
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c13355
XDG_SESSION_TYPE=unspecified

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package tvc
dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-4+b3
dpkg-buildpackage: info: source distribution bookworm-staging
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
	cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf ..
CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  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 12.1.0
-- The CXX compiler identification is GNU 12.1.0
-- 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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2'
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_EXPORT_NO_PACKAGE_REGISTRY
    CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
    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  -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make  -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make  -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[  3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o
[  3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.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 -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
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/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 -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
/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 -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
[  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 -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
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/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 -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/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 -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
/<<PKGBUILDDIR>>/VariantCaller/VariantCaller.cpp: In function ‘void TheSilenceOfTheArmadillos(std::ofstream&)’:
/<<PKGBUILDDIR>>/VariantCaller/VariantCaller.cpp:36:24: warning: ‘void arma::set_stream_err1(std::ostream&)’ is deprecated [-Wdeprecated-declarations]
   36 |   arma::set_stream_err1(null_ostream);
      |   ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/armadillo:384,
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   92 | set_stream_err1(std::ostream& user_stream)
      | ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/VariantCaller/VariantCaller.cpp:37:24: warning: ‘void arma::set_stream_err2(std::ostream&)’ is deprecated [-Wdeprecated-declarations]
   37 |   arma::set_stream_err2(null_ostream);
      |   ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/armadillo_bits/debug.hpp:103:1: note: declared here
  103 | set_stream_err2(std::ostream& user_stream)
      | ^~~~~~~~~~~~~~~
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/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 -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/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 -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
[ 15%] 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 -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
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/Util/OptArgs.h:11,
                 from /<<PKGBUILDDIR>>/Util/OptArgs.cpp:4:
/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
  439 |       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++/12/bits/stl_vector.h:1294:21,
    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++/12/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 -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/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 -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
[ 20%] 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 -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
[ 21%] 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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -o tvcassembly  -lbamtools -lz -lpthread -ljsoncpp 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 21%] Built target tvcassembly
[ 23%] 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 -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
[ 25%] 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 -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
[ 26%] 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 -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
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/Util/OptArgs.h:11,
                 from /<<PKGBUILDDIR>>/Util/OptArgs.cpp:4:
/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
  439 |       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++/12/bits/stl_vector.h:1294:21,
    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++/12/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 /<<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++/12/string:47,
                 from /<<PKGBUILDDIR>>/VariantCaller/tvcutils/unify_vcf.cpp:7:
/usr/include/c++/12/bits/stl_iterator.h:458:5: note: declared here
  458 |     operator!=(const reverse_iterator<_Iterator>& __x,
      |     ^~~~~~~~
[ 28%] 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 -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
[ 29%] 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 -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
[ 31%] 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 -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
[ 32%] 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 -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++/12/vector:70,
                 from /<<PKGBUILDDIR>>/VariantCaller/tvcutils/unify_vcf.cpp:13:
/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<markov_state>::iterator’ changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/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++/12/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++/12/bits/stl_vector.h:1294:21,
    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++/12/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)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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 -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 -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 -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 -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 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 -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;
      |                                          ^~~~~~~~
[ 42%] 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 -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
[ 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 -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 -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/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 -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
[ 48%] 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 -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
[ 50%] 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 -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'
[ 50%] Built target tvcutils
[ 51%] 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 -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
[ 53%] 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 -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
In file included from /usr/include/c++/12/map:60,
                 from /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/InputStructures.h:14,
                 from /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/InputStructures.cpp:7:
/usr/include/c++/12/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++/12/bits/stl_tree.h:2457:7: 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
 2457 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 54%] 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 -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
In file included from /usr/include/c++/12/vector:70,
                 from /<<PKGBUILDDIR>>/VariantCaller/Bookkeeping/InputStructures.h:12:
/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<DPTreephaser>::iterator’ changed in GCC 7.1
  439 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
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++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<DPTreephaser*, std::vector<DPTreephaser> >’ changed in GCC 7.1
 1287 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
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++/12/bits/stl_map.h:858:27,
    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++/12/bits/stl_map.h:638:45: 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
  638 |           return _M_t._M_emplace_hint_unique(__pos,
      |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
  639 |                                              std::forward<_Args>(__args)...);
      |                                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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 -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 -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 -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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[ 64%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o
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[ 65%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o
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[ 67%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o
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[ 68%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o
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[ 70%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o
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[ 71%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o
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[ 73%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o
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[ 75%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o
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[ 76%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o
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[ 78%] Building CXX object CMakeFiles/tvc.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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/split.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -c /<<PKGBUILDDIR>>/external/vcflib/split.cpp
[ 79%] Building CXX object CMakeFiles/tvc.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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<<PKGBUILDDIR>>/external/vcflib/tabixpp/tabix.cpp
[ 81%] Building C object CMakeFiles/tvc.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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -c /<<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;
      |                                          ^~~~~~~~
[ 82%] Building C object CMakeFiles/tvc.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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -c /<<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);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 84%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o
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[ 85%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o
/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -c /<<PKGBUILDDIR>>/BaseCaller/PIDloop.cpp
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/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 -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
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[ 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 -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 -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
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/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 -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 -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 -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 -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++/12/vector:70,
                 from /<<PKGBUILDDIR>>/Util/OptArgs.h:11,
                 from /<<PKGBUILDDIR>>/Util/OptArgs.cpp:4:
/usr/include/c++/12/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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
  439 |       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++/12/bits/stl_vector.h:1294:21,
    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++/12/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 -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
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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
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
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: 
1/8 Test #1: tvc_call .........................................   Passed    0.06 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
2/8 Test #4: tvcutils_call ....................................   Passed    0.07 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    0.04 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
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    0.04 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
2: Recalibration was detected from comment lines in bam file(s):
2: 1 unique blocks of recalibration info detected.
2: Loading systematic error contexts.
7: Parameter novel-tvc-vcf is required and empty.
7: 
7: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
7: 
7: Usage:   tvcutils unify_vcf [options]
7: 
7: General options:
7:   -t,--novel-tvc-vcf             FILE       small variants VCF file produced by TVC (required)
7:   -i,--novel-assembly-vcf        FILE       long indels VCF file produced by TVCASSEMBLY (optional)
7:   -a,--hotspot-annotation-vcf    FILE       hotspot annotations VCF file (optional)
7:   -a,--hotspot-annotation-vcf    FILE       hotspot annotations VCF file (optional)
7:   -f,--reference-fasta           FILE       FASTA file containing reference genome (required)
7:   -b,--target-file               FILE       target regions BED file (optional)
7:   -o,--output-vcf                FILE       output merged and annotated VCF or VCF.GZ file (required)
7:   -j,--tvc-metrics               FILE       JSON file with tvc metrics (optional)
7:   -d,--input-depth               FILE       output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok)
7:   -m,--min-depth                 INT        minimum coverage depth in GVCF output (optional)
7: 
5/8 Test #7: tvcutils_unify_vcf_call ..........................   Passed    0.05 sec
3: Recalibration was detected from comment lines in bam file(s):
3: 1 unique blocks of recalibration info detected.
3: Loading systematic error contexts.
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    0.04 sec
2: Loaded.
3: Loaded.
2: Recalibration model: suppressed
2: 
2: 
2: [tvc] Normal termination. Processing time: 4 seconds.
3: 
3: 
3: [tvc] Normal termination. Processing time: 4 seconds.
7/8 Test #2: tvc_test_1_thread_sse_off ........................   Passed    4.25 sec
8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ...   Passed    4.36 sec

100% tests passed, 0 tests failed out of 8

Total Test time (real) =   4.38 sec
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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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=
Consolidate compiler generated dependencies of target tvcassembly
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make  -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 10%] Built target tvcassembly
Consolidate compiler generated dependencies of target tvcutils
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make  -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 31%] Built target tvcutils
Consolidate compiler generated dependencies of target tvc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make  -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'.
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  -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: debian/tvc/usr/bin/tvcassembly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcutils contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcassembly debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc were not linked against libdisorder.so.0 (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-4+b3_armhf.deb'.
dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-4+b3_armhf.deb'.
 dpkg-genbuildinfo --build=any -O../tvc_5.0.3+git20151221.80e144e+dfsg-4+b3_armhf.buildinfo
 dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../tvc_5.0.3+git20151221.80e144e+dfsg-4+b3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-09-05T17:10:15Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


tvc_5.0.3+git20151221.80e144e+dfsg-4+b3_armhf.changes:
------------------------------------------------------

Format: 1.8
Date: Mon, 05 Sep 2022 17:00:04 +0000
Source: tvc (5.0.3+git20151221.80e144e+dfsg-4)
Binary: tvc tvc-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 5.0.3+git20151221.80e144e+dfsg-4+b3
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Raspbian pi4 based autobuilder <root@raspbian.org>
Description:
 tvc        - genetic variant caller for Ion Torrent sequencing platforms
Changes:
 tvc (5.0.3+git20151221.80e144e+dfsg-4+b3) bookworm-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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Checksums-Sha256:
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Files:
 ede5d627e963814f17ef37c554e03b06 11120836 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b3_armhf.deb
 925d1d84b5480c16549b3aef804b8003 8204 science optional tvc_5.0.3+git20151221.80e144e+dfsg-4+b3_armhf.buildinfo
 b3be050d7524fe4958516521aa8d0ba0 941560 science optional tvc_5.0.3+git20151221.80e144e+dfsg-4+b3_armhf.deb

+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: tvc (5.0.3+git20151221.80e144e+dfsg-4)
Binary: tvc tvc-dbgsym
Architecture: armhf
Version: 5.0.3+git20151221.80e144e+dfsg-4+b3
Binary-Only-Changes:
 tvc (5.0.3+git20151221.80e144e+dfsg-4+b3) bookworm-staging; urgency=low, binary-only=yes
 .
   * Binary-only non-maintainer upload for armhf; no source changes.
   * rebuild due to debcheck failure
 .
  -- Raspbian pi4 based autobuilder <root@raspbian.org>  Mon, 05 Sep 2022 17:00:04 +0000
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Mon, 05 Sep 2022 17:10:13 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 adduser (= 3.123),
 autoconf (= 2.71-2),
 automake (= 1:1.16.5-1.3),
 autopoint (= 0.21-8),
 autotools-dev (= 20220109.1),
 base-files (= 12.2+rpi1),
 base-passwd (= 3.6.0),
 bash (= 5.1-6.1),
 binutils (= 2.38.90.20220713-2+rpi1),
 binutils-arm-linux-gnueabihf (= 2.38.90.20220713-2+rpi1),
 binutils-common (= 2.38.90.20220713-2+rpi1),
 bsdextrautils (= 2.38.1-1),
 bsdutils (= 1:2.38.1-1),
 build-essential (= 12.9),
 bzip2 (= 1.0.8-5+b2),
 cmake (= 3.24.1-1),
 cmake-data (= 3.24.1-1),
 coreutils (= 8.32-4.1),
 cpp (= 4:12.1.0-3+rpi1),
 cpp-12 (= 12.1.0-8+rpi1),
 dash (= 0.5.11+git20210903+057cd650a4ed-8),
 debconf (= 1.5.79),
 debhelper (= 13.9.1),
 debianutils (= 5.7-0.3),
 dh-autoreconf (= 20),
 dh-elpa-helper (= 2.0.10),
 dh-strip-nondeterminism (= 1.13.0-1),
 diffutils (= 1:3.8-1),
 dmsetup (= 2:1.02.185-1),
 dpkg (= 1.21.9+rpi1),
 dpkg-dev (= 1.21.9+rpi1),
 dwz (= 0.14-1),
 emacsen-common (= 3.0.4),
 file (= 1:5.41-4),
 findutils (= 4.9.0-3),
 g++ (= 4:12.1.0-3+rpi1),
 g++-12 (= 12.1.0-8+rpi1),
 gcc (= 4:12.1.0-3+rpi1),
 gcc-12 (= 12.1.0-8+rpi1),
 gcc-12-base (= 12.1.0-8+rpi1),
 gettext (= 0.21-8),
 gettext-base (= 0.21-8),
 grep (= 3.7-1),
 groff-base (= 1.22.4-8),
 gzip (= 1.12-1),
 hdf5-helpers (= 1.10.7+repack-4+rpi1+b1),
 hostname (= 3.23),
 init-system-helpers (= 1.64),
 intltool-debian (= 0.35.0+20060710.5),
 libacl1 (= 2.3.1-1),
 libaec-dev (= 1.0.6-1),
 libaec0 (= 1.0.6-1),
 libapparmor1 (= 3.0.7-1),
 libarchive-zip-perl (= 1.68-1),
 libarchive13 (= 3.6.0-1),
 libargon2-1 (= 0~20171227-0.3),
 libarmadillo-dev (= 1:11.2.3+dfsg-1),
 libarmadillo11 (= 1:11.2.3+dfsg-1),
 libarpack2 (= 3.8.0-1),
 libarpack2-dev (= 3.8.0-1),
 libasan8 (= 12.1.0-8+rpi1),
 libatomic1 (= 12.1.0-8+rpi1),
 libattr1 (= 1:2.5.1-1),
 libaudit-common (= 1:3.0.7-1),
 libaudit1 (= 1:3.0.7-1+b1),
 libbamtools-dev (= 2.5.2+dfsg-2),
 libbamtools2.5.2 (= 2.5.2+dfsg-2),
 libbinutils (= 2.38.90.20220713-2+rpi1),
 libblas-dev (= 3.10.1-2),
 libblas3 (= 3.10.1-2),
 libblkid1 (= 2.38.1-1),
 libboost-math-dev (= 1.74.0.3+b4),
 libboost-math1.74-dev (= 1.74.0-17),
 libboost-math1.74.0 (= 1.74.0-17),
 libboost1.74-dev (= 1.74.0-17),
 libbrotli1 (= 1.0.9-2+b2),
 libbz2-1.0 (= 1.0.8-5+b2),
 libc-bin (= 2.33-8+rpi1),
 libc-dev-bin (= 2.33-8+rpi1),
 libc6 (= 2.33-8+rpi1),
 libc6-dev (= 2.33-8+rpi1),
 libcap-ng0 (= 0.8.3-1),
 libcap2 (= 1:2.44-1),
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 libcrypt-dev (= 1:4.4.28-2),
 libcrypt1 (= 1:4.4.28-2),
 libcryptsetup12 (= 2:2.5.0-2),
 libctf-nobfd0 (= 2.38.90.20220713-2+rpi1),
 libctf0 (= 2.38.90.20220713-2+rpi1),
 libcurl4 (= 7.84.0-2),
 libcurl4-openssl-dev (= 7.84.0-2),
 libdb5.3 (= 5.3.28+dfsg1-0.10),
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 libdebhelper-perl (= 13.9.1),
 libdevmapper1.02.1 (= 2:1.02.185-1),
 libdisorder-dev (= 0.0.2+git20130809.8062ee1-4),
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 libdpkg-perl (= 1.21.9+rpi1),
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 libexpat1 (= 2.4.8-1),
 libfdisk1 (= 2.38.1-1),
 libffi8 (= 3.4.2-4),
 libfile-stripnondeterminism-perl (= 1.13.0-1),
 libgcc-12-dev (= 12.1.0-8+rpi1),
 libgcc-s1 (= 12.1.0-8+rpi1),
 libgcrypt20 (= 1.10.1-2+b2),
 libgdbm-compat4 (= 1.23-1),
 libgdbm6 (= 1.23-1),
 libgfortran5 (= 12.1.0-8+rpi1),
 libgmp10 (= 2:6.2.1+dfsg1-1),
 libgnutls30 (= 3.7.7-2),
 libgomp1 (= 12.1.0-8+rpi1),
 libgpg-error0 (= 1.45-2),
 libgssapi-krb5-2 (= 1.20-1),
 libhdf5-103-1 (= 1.10.7+repack-4+rpi1+b1),
 libhdf5-cpp-103-1 (= 1.10.7+repack-4+rpi1+b1),
 libhdf5-dev (= 1.10.7+repack-4+rpi1+b1),
 libhdf5-fortran-102 (= 1.10.7+repack-4+rpi1+b1),
 libhdf5-hl-100 (= 1.10.7+repack-4+rpi1+b1),
 libhdf5-hl-cpp-100 (= 1.10.7+repack-4+rpi1+b1),
 libhdf5-hl-fortran-100 (= 1.10.7+repack-4+rpi1+b1),
 libhogweed6 (= 3.8.1-2),
 libicu71 (= 71.1-3),
 libidn2-0 (= 2.3.3-1),
 libip4tc2 (= 1.8.8-1),
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 libjpeg-dev (= 1:2.1.2-1),
 libjpeg62-turbo (= 1:2.1.2-1),
 libjpeg62-turbo-dev (= 1:2.1.2-1),
 libjson-c5 (= 0.16-1),
 libjsoncpp-dev (= 1.9.5-4),
 libjsoncpp25 (= 1.9.5-4),
 libk5crypto3 (= 1.20-1),
 libkeyutils1 (= 1.6.3-1),
 libkmod2 (= 30+20220630-3),
 libkrb5-3 (= 1.20-1),
 libkrb5support0 (= 1.20-1),
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 liblapack3 (= 3.10.1-2),
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 libmagic-mgc (= 1:5.41-4),
 libmagic1 (= 1:5.41-4),
 libmount1 (= 2.38.1-1),
 libmpc3 (= 1.2.1-2),
 libmpfr6 (= 4.1.0-3),
 libncurses6 (= 6.3+20220423-2),
 libncursesw6 (= 6.3+20220423-2),
 libnettle8 (= 3.8.1-2),
 libnghttp2-14 (= 1.49.0-1),
 libnsl-dev (= 1.3.0-2),
 libnsl2 (= 1.3.0-2),
 libp11-kit0 (= 0.24.1-1),
 libpam-modules (= 1.5.2-2),
 libpam-modules-bin (= 1.5.2-2),
 libpam-runtime (= 1.5.2-2),
 libpam0g (= 1.5.2-2),
 libpcre2-8-0 (= 10.40-1+b2),
 libpcre3 (= 2:8.39-14),
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 libpsl5 (= 0.21.0-1.2),
 librhash0 (= 1.4.3-3),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
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 libsasl2-modules-db (= 2.1.28+dfsg-7),
 libseccomp2 (= 2.5.4-1+rpi1),
 libselinux1 (= 3.4-1),
 libsemanage-common (= 3.4-1),
 libsemanage2 (= 3.4-1),
 libsepol2 (= 3.4-2),
 libsmartcols1 (= 2.38.1-1),
 libsmithwaterman-dev (= 0.0+git20160702.2610e25-12),
 libsmithwaterman0 (= 0.0+git20160702.2610e25-12),
 libssh2-1 (= 1.10.0-3+b1),
 libssl-dev (= 3.0.5-2),
 libssl3 (= 3.0.5-2),
 libstdc++-12-dev (= 12.1.0-8+rpi1),
 libstdc++6 (= 12.1.0-8+rpi1),
 libsub-override-perl (= 0.09-3),
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 libsuperlu5 (= 5.3.0+dfsg1-2),
 libsystemd-shared (= 251.3-1+rpi1),
 libsystemd0 (= 251.3-1+rpi1),
 libsz2 (= 1.0.6-1),
 libtasn1-6 (= 4.18.0-4),
 libtinfo6 (= 6.3+20220423-2),
 libtirpc-common (= 1.3.3+ds-1),
 libtirpc-dev (= 1.3.3+ds-1),
 libtirpc3 (= 1.3.3+ds-1),
 libtool (= 2.4.7-4),
 libubsan1 (= 12.1.0-8+rpi1),
 libuchardet0 (= 0.0.7-1),
 libudev1 (= 251.3-1+rpi1),
 libunistring2 (= 1.0-1),
 libuuid1 (= 2.38.1-1),
 libuv1 (= 1.44.1-2+rpi1),
 libxml2 (= 2.9.14+dfsg-1),
 libzstd1 (= 1.5.2+dfsg-1),
 linux-libc-dev (= 5.18.14-1+rpi1),
 login (= 1:4.11.1+dfsg1-2),
 lsb-base (= 11.2+rpi1),
 m4 (= 1.4.19-1),
 make (= 4.3-4.1),
 man-db (= 2.10.2-2),
 mawk (= 1.3.4.20200120-3.1),
 mount (= 2.38.1-1),
 ncurses-base (= 6.3+20220423-2),
 ncurses-bin (= 6.3+20220423-2),
 passwd (= 1:4.11.1+dfsg1-2),
 patch (= 2.7.6-7),
 perl (= 5.34.0-5),
 perl-base (= 5.34.0-5),
 perl-modules-5.34 (= 5.34.0-5),
 po-debconf (= 1.0.21+nmu1),
 procps (= 2:3.3.17-7),
 rpcsvc-proto (= 1.4.2-4),
 sed (= 4.8-1),
 sensible-utils (= 0.0.17),
 sgml-base (= 1.30),
 systemd (= 251.3-1+rpi1),
 sysvinit-utils (= 3.04-1),
 tar (= 1.34+dfsg-1),
 util-linux (= 2.38.1-1),
 util-linux-extra (= 2.38.1-1),
 xz-utils (= 5.2.5-2.1),
 zlib1g (= 1:1.2.11.dfsg-4.1),
 zlib1g-dev (= 1:1.2.11.dfsg-4.1)
Environment:
 DEB_BUILD_OPTIONS="parallel=4"
 LANG="en_GB.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1662397204"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b3_armhf.deb
--------------------------------------------------------

 new Debian package, version 2.0.
 size 11120836 bytes: control archive=720 bytes.
     529 bytes,    12 lines      control              
     401 bytes,     4 lines      md5sums              
 Package: tvc-dbgsym
 Source: tvc (5.0.3+git20151221.80e144e+dfsg-4)
 Version: 5.0.3+git20151221.80e144e+dfsg-4+b3
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 11180
 Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-4+b3)
 Section: debug
 Priority: optional
 Description: debug symbols for tvc
 Build-Ids: 48ed2618b5a2de05fcd4f2392a856ccea496ca5c 8591ee9d19426b489dd72470e4ae640cefefc965 c1d19d95909e82edf470ec8cf5aaaaaff0421977

drwxr-xr-x root/root         0 2022-09-05 17:00 ./
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/lib/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/lib/debug/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/lib/debug/.build-id/48/
-rw-r--r-- root/root   2258640 2022-09-05 17:00 ./usr/lib/debug/.build-id/48/ed2618b5a2de05fcd4f2392a856ccea496ca5c.debug
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/lib/debug/.build-id/85/
-rw-r--r-- root/root    826836 2022-09-05 17:00 ./usr/lib/debug/.build-id/85/91ee9d19426b489dd72470e4ae640cefefc965.debug
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/lib/debug/.build-id/c1/
-rw-r--r-- root/root   7868668 2022-09-05 17:00 ./usr/lib/debug/.build-id/c1/d19d95909e82edf470ec8cf5aaaaaff0421977.debug
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root    477504 2022-09-05 17:00 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/tvc.debug
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/doc/
lrwxrwxrwx root/root         0 2022-09-05 17:00 ./usr/share/doc/tvc-dbgsym -> tvc


tvc_5.0.3+git20151221.80e144e+dfsg-4+b3_armhf.deb
-------------------------------------------------

 new Debian package, version 2.0.
 size 941560 bytes: control archive=1724 bytes.
    1044 bytes,    17 lines      control              
    2537 bytes,    29 lines      md5sums              
 Package: tvc
 Source: tvc (5.0.3+git20151221.80e144e+dfsg-4)
 Version: 5.0.3+git20151221.80e144e+dfsg-4+b3
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3089
 Depends: libarmadillo11 (>= 1:11.2.3+dfsg), libbamtools2.5.2 (>= 2.5.2+dfsg), libc6 (>= 2.33), libdisorder0 (>= 0.0.2), libgcc-s1 (>= 3.5), libjsoncpp25 (>= 1.9.5), libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 11), zlib1g (>= 1:1.1.4), python3
 Section: science
 Priority: optional
 Homepage: http://ioncommunity.thermofisher.com
 Description: genetic variant caller for Ion Torrent sequencing platforms
  Torrent Variant Caller (TVC) is a genetic variant caller for
  Ion Torrent sequencing platforms, and is specially optimized to exploit the
  underlying flow signal information in the statistical model
  to evaluate variants. Torrent Variant Caller is designed to call
  single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs),
  insertions, deletions, and block substitutions.

drwxr-xr-x root/root         0 2022-09-05 17:00 ./
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/bin/
-rwxr-xr-x root/root    987128 2022-09-05 17:00 ./usr/bin/tvc
-rwxr-xr-x root/root    198960 2022-09-05 17:00 ./usr/bin/tvcassembly
-rwxr-xr-x root/root    526924 2022-09-05 17:00 ./usr/bin/tvcutils
-rwxr-xr-x root/root     12985 2022-09-05 17:00 ./usr/bin/variant_caller_pipeline.py
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/TVC/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/TVC/examples/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/TVC/examples/example1/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/TVC/examples/example1/expected/
-rw-r--r-- root/root      6876 2015-12-21 20:38 ./usr/share/TVC/examples/example1/expected/TSVC_variants.vcf
-rw-r--r-- root/root      6479 2015-12-21 20:38 ./usr/share/TVC/examples/example1/expected/small_variants.vcf
-rw-r--r-- root/root       108 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.dict
-rw-r--r-- root/root      3400 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.fasta
-rw-r--r-- root/root        22 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.fasta.fai
-rw-r--r-- root/root    225904 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bam
-rw-r--r-- root/root        96 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bam.bai
-rw-r--r-- root/root        13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bed
-rw-r--r-- root/root        13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_merged_plain.bed
-rw-r--r-- root/root        13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_original.bed
-rw-r--r-- root/root        70 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_unmerged_detail.bed
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/TVC/pluginMedia/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/TVC/pluginMedia/parameter_sets/
-rw-r--r-- root/root      2809 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json
-rw-r--r-- root/root      2926 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
-rw-r--r-- root/root      2826 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json
-rw-r--r-- root/root      2918 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json
-rw-r--r-- root/root      3062 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json
-rw-r--r-- root/root      2628 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json
-rw-r--r-- root/root      2757 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/TVC/sse/
-rw-r--r-- root/root    683778 2015-12-21 20:38 ./usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt
-rw-r--r-- root/root    451754 2015-12-21 20:38 ./usr/share/TVC/sse/motifset.txt
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/doc/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/doc/tvc/
-rw-r--r-- root/root      1078 2021-10-31 14:47 ./usr/share/doc/tvc/README.Debian
-rw-r--r-- root/root       234 2022-09-05 17:00 ./usr/share/doc/tvc/changelog.Debian.armhf.gz
-rw-r--r-- root/root      1240 2022-09-05 17:00 ./usr/share/doc/tvc/changelog.Debian.gz
-rw-r--r-- root/root      2939 2021-10-31 14:47 ./usr/share/doc/tvc/copyright
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/lintian/
drwxr-xr-x root/root         0 2022-09-05 17:00 ./usr/share/lintian/overrides/
-rw-r--r-- root/root       135 2021-10-31 14:47 ./usr/share/lintian/overrides/tvc


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build Type: any
Build-Space: 141916
Build-Time: 610
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 752
Job: tvc_5.0.3+git20151221.80e144e+dfsg-4
Machine Architecture: armhf
Package: tvc
Package-Time: 1409
Source-Version: 5.0.3+git20151221.80e144e+dfsg-4
Space: 141916
Status: successful
Version: 5.0.3+git20151221.80e144e+dfsg-4+b3
--------------------------------------------------------------------------------
Finished at 2022-09-05T17:10:15Z
Build needed 00:23:29, 141916k disk space