tvc →
5.0.3+git20151221.80e144e+dfsg-4+b2 →
armhf → 2022-06-18 17:16:15
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+=================================================================================+
| tvc 5.0.3+git20151221.80e144e+dfsg-4+b2 (armhf) Sat, 18 Jun 2022 17:05:29 +0000 |
+=================================================================================+
Package: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-4+b2
Source Version: 5.0.3+git20151221.80e144e+dfsg-4
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-57a27077-f4af-4c33-8e5d-a918334280dc' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.1 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.0 MB]
Fetched 27.0 MB in 10s (2623 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/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 (6942 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/tvc-pTIkqc/tvc-5.0.3+git20151221.80e144e+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/tvc-pTIkqc' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-x66csE/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-x66csE/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-x66csE/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (9389 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 73 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (72.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12621 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev
Filtered Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev
dpkg-deb: building package 'sbuild-build-depends-tvc-dummy' in '/<<BUILDDIR>>/resolver-x66csE/apt_archive/sbuild-build-depends-tvc-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-tvc-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ Sources [535 B]
Get:5 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ Packages [619 B]
Fetched 2487 B in 0s (12.4 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install tvc build dependencies (apt-based resolver)
---------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file gcc-12-base gettext gettext-base groff-base hdf5-helpers
intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13
libarmadillo-dev libarmadillo11 libarpack2 libarpack2-dev libatomic1
libbamtools-dev libbamtools2.5.1 libblas-dev libblas3 libboost-math-dev
libboost-math1.74-dev libboost-math1.74.0 libboost1.74-dev libbrotli1
libcc1-0 libcurl4 libcurl4-openssl-dev libdebhelper-perl libdisorder-dev
libdisorder0 libelf1 libexpat1 libfile-stripnondeterminism-perl libgcc-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 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev
libjsoncpp25 liblapack-dev liblapack3 libmagic-mgc libmagic1 libncurses6
libncursesw6 libnghttp2-14 libpipeline1 libprocps8 libpsl5 librhash0
librtmp1 libsigsegv2 libsmithwaterman-dev libsmithwaterman0 libssh2-1
libssl-dev libssl3 libstdc++6 libsub-override-perl libsuperlu-dev
libsuperlu5 libsz2 libtinfo6 libtool libubsan1 libuchardet0 libuv1 libxml2
m4 man-db po-debconf procps sgml-base zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build
cmake-format dh-make 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 libsuperlu-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl sgml-base-doc
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libgpm2 publicsuffix
libltdl-dev libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file gettext gettext-base groff-base hdf5-helpers
intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13
libarmadillo-dev libarmadillo11 libarpack2 libarpack2-dev libbamtools-dev
libbamtools2.5.1 libblas-dev libblas3 libboost-math-dev
libboost-math1.74-dev libboost-math1.74.0 libboost1.74-dev libbrotli1
libcurl4 libcurl4-openssl-dev libdebhelper-perl libdisorder-dev libdisorder0
libelf1 libexpat1 libfile-stripnondeterminism-perl 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
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev libjsoncpp25
liblapack-dev liblapack3 libmagic-mgc libmagic1 libncurses6 libnghttp2-14
libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2
libsmithwaterman-dev libsmithwaterman0 libssh2-1 libssl-dev libssl3
libsub-override-perl libsuperlu-dev libsuperlu5 libsz2 libtool libuchardet0
libuv1 libxml2 m4 man-db po-debconf procps sbuild-build-depends-tvc-dummy
sgml-base zlib1g-dev
The following packages will be upgraded:
gcc-12-base libatomic1 libcc1-0 libgcc-s1 libgomp1 libncursesw6 libstdc++6
libtinfo6 libubsan1 zlib1g
10 upgraded, 90 newly installed, 0 to remove and 63 not upgraded.
Need to get 53.4 MB of archives.
After this operation, 319 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-x66csE/apt_archive ./ sbuild-build-depends-tvc-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf sgml-base all 1.30 [15.1 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-4+b2 [84.5 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libatomic1 armhf 12.1.0-2+rpi1 [8196 B]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libubsan1 armhf 12.1.0-2+rpi1 [860 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf gcc-12-base armhf 12.1.0-2+rpi1 [207 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libstdc++6 armhf 12.1.0-2+rpi1 [504 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libgomp1 armhf 12.1.0-2+rpi1 [95.4 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libcc1-0 armhf 12.1.0-2+rpi1 [32.1 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libgcc-s1 armhf 12.1.0-2+rpi1 [36.1 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libtinfo6 armhf 6.3+20220423-2 [337 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libncursesw6 armhf 6.3+20220423-2 [104 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38-4 [137 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-1 [33.7 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-1 [1362 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-7 [60.7 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-7 [475 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-6 [171 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-6 [510 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libarchive13 armhf 3.6.0-1 [306 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.47.0-1+b1 [65.3 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libssl3 armhf 3.0.3-7 [1645 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.83.1-2 [317 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.8-1 [84.1 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp25 armhf 1.9.5-4 [66.7 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf librhash0 armhf 1.4.2-1 [141 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libuv1 armhf 1.44.1-2+rpi1 [124 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf dh-elpa-helper all 2.0.10 [11.3 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf emacsen-common all 3.0.4 [19.3 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf cmake-data all 3.23.2-1 [1939 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf cmake armhf 3.23.2-1 [3551 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.7.1 [195 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-1 [175 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-6 [1214 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.7.1 [1071 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf hdf5-helpers armhf 1.10.7+repack-4+rpi1+b1 [43.2 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libaec0 armhf 1.0.6-1 [19.3 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libsz2 armhf 1.0.6-1 [7452 B]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libaec-dev armhf 1.0.6-1 [17.6 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.1.0-2+rpi1 [238 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libarpack2 armhf 3.8.0-1 [85.9 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libsuperlu5 armhf 5.3.0+dfsg1-2 [128 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libarmadillo11 armhf 1:11.1.1+dfsg-3 [99.5 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.1-2 [114 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.1-2 [2847 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libarpack2-dev armhf 3.8.0-1 [94.6 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-103-1 armhf 1.10.7+repack-4+rpi1+b1 [1240 kB]
Get:76 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:77 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:78 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:79 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:80 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:81 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4+b2 [183 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.2-1 [261 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.1.2-1 [74.7 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-openssl-dev armhf 7.83.1-2 [394 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 3.0.3-7 [2122 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-dev armhf 1.10.7+repack-4+rpi1+b1 [2208 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libsuperlu-dev armhf 5.3.0+dfsg1-2 [22.1 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libarmadillo-dev armhf 1:11.1.1+dfsg-3 [403 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-10+b1 [135 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-10+b1 [178 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-16 [9536 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libboost-math1.74.0 armhf 1.74.0-16 [343 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libboost-math1.74-dev armhf 1.74.0-16 [400 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libboost-math-dev armhf 1.74.0.3+b4 [4808 B]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-4 [4856 B]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-4 [4484 B]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp-dev armhf 1.9.5-4 [26.4 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12 [32.4 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-12 [36.7 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 53.4 MB in 6s (9286 kB/s)
Selecting previously unselected package sgml-base.
(Reading database ... 12621 files and directories currently installed.)
Preparing to unpack .../sgml-base_1.30_all.deb ...
Unpacking sgml-base (1.30) ...
Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-4+b2_armhf.deb ...
Unpacking zlib1g:armhf (1:1.2.11.dfsg-4+b2) over (1:1.2.11.dfsg-4) ...
Setting up zlib1g:armhf (1:1.2.11.dfsg-4+b2) ...
(Reading database ... 12650 files and directories currently installed.)
Preparing to unpack .../libatomic1_12.1.0-2+rpi1_armhf.deb ...
Unpacking libatomic1:armhf (12.1.0-2+rpi1) over (12-20220319-1+rpi1) ...
Preparing to unpack .../libubsan1_12.1.0-2+rpi1_armhf.deb ...
Unpacking libubsan1:armhf (12.1.0-2+rpi1) over (12-20220319-1+rpi1) ...
Preparing to unpack .../gcc-12-base_12.1.0-2+rpi1_armhf.deb ...
Unpacking gcc-12-base:armhf (12.1.0-2+rpi1) over (12-20220319-1+rpi1) ...
Setting up gcc-12-base:armhf (12.1.0-2+rpi1) ...
(Reading database ... 12650 files and directories currently installed.)
Preparing to unpack .../libstdc++6_12.1.0-2+rpi1_armhf.deb ...
Unpacking libstdc++6:armhf (12.1.0-2+rpi1) over (12-20220319-1+rpi1) ...
Setting up libstdc++6:armhf (12.1.0-2+rpi1) ...
(Reading database ... 12650 files and directories currently installed.)
Preparing to unpack .../libgomp1_12.1.0-2+rpi1_armhf.deb ...
Unpacking libgomp1:armhf (12.1.0-2+rpi1) over (12-20220319-1+rpi1) ...
Preparing to unpack .../libcc1-0_12.1.0-2+rpi1_armhf.deb ...
Unpacking libcc1-0:armhf (12.1.0-2+rpi1) over (12-20220319-1+rpi1) ...
Preparing to unpack .../libgcc-s1_12.1.0-2+rpi1_armhf.deb ...
Unpacking libgcc-s1:armhf (12.1.0-2+rpi1) over (12-20220319-1+rpi1) ...
Setting up libgcc-s1:armhf (12.1.0-2+rpi1) ...
(Reading database ... 12650 files and directories currently installed.)
Preparing to unpack .../libtinfo6_6.3+20220423-2_armhf.deb ...
Unpacking libtinfo6:armhf (6.3+20220423-2) over (6.3-2) ...
Setting up libtinfo6:armhf (6.3+20220423-2) ...
(Reading database ... 12649 files and directories currently installed.)
Preparing to unpack .../libncursesw6_6.3+20220423-2_armhf.deb ...
Unpacking libncursesw6:armhf (6.3+20220423-2) over (6.3-2) ...
Setting up libncursesw6:armhf (6.3+20220423-2) ...
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12649 files and directories currently installed.)
Preparing to unpack .../00-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../01-groff-base_1.22.4-8_armhf.deb ...
Unpacking groff-base (1.22.4-8) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../02-bsdextrautils_2.38-4_armhf.deb ...
Unpacking bsdextrautils (2.38-4) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.5.6-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.6-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.10.2-1_armhf.deb ...
Unpacking man-db (2.10.2-1) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../05-libncurses6_6.3+20220423-2_armhf.deb ...
Unpacking libncurses6:armhf (6.3+20220423-2) ...
Selecting previously unselected package libprocps8:armhf.
Preparing to unpack .../06-libprocps8_2%3a3.3.17-7_armhf.deb ...
Unpacking libprocps8:armhf (2:3.3.17-7) ...
Selecting previously unselected package procps.
Preparing to unpack .../07-procps_2%3a3.3.17-7_armhf.deb ...
Unpacking procps (2:3.3.17-7) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../08-libmagic-mgc_1%3a5.41-4_armhf.deb ...
Unpacking libmagic-mgc (1:5.41-4) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../09-libmagic1_1%3a5.41-4_armhf.deb ...
Unpacking libmagic1:armhf (1:5.41-4) ...
Selecting previously unselected package file.
Preparing to unpack .../10-file_1%3a5.41-4_armhf.deb ...
Unpacking file (1:5.41-4) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../11-gettext-base_0.21-6_armhf.deb ...
Unpacking gettext-base (0.21-6) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../12-libsigsegv2_2.14-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.14-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../13-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../14-autoconf_2.71-2_all.deb ...
Unpacking autoconf (2.71-2) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../16-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../17-autopoint_0.21-6_all.deb ...
Unpacking autopoint (0.21-6) ...
Selecting previously unselected package libicu71:armhf.
Preparing to unpack .../18-libicu71_71.1-3_armhf.deb ...
Unpacking libicu71:armhf (71.1-3) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../19-libxml2_2.9.14+dfsg-1_armhf.deb ...
Unpacking libxml2:armhf (2.9.14+dfsg-1) ...
Selecting previously unselected package libarchive13:armhf.
Preparing to unpack .../20-libarchive13_3.6.0-1_armhf.deb ...
Unpacking libarchive13:armhf (3.6.0-1) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../21-libbrotli1_1.0.9-2+b2_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.9-2+b2) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../22-libnghttp2-14_1.47.0-1+b1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.47.0-1+b1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../23-libpsl5_0.21.0-1.2_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1.2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../24-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssl3:armhf.
Preparing to unpack .../25-libssl3_3.0.3-7_armhf.deb ...
Unpacking libssl3:armhf (3.0.3-7) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../26-libssh2-1_1.10.0-3+b1_armhf.deb ...
Unpacking libssh2-1:armhf (1.10.0-3+b1) ...
Selecting previously unselected package libcurl4:armhf.
Preparing to unpack .../27-libcurl4_7.83.1-2_armhf.deb ...
Unpacking libcurl4:armhf (7.83.1-2) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../28-libexpat1_2.4.8-1_armhf.deb ...
Unpacking libexpat1:armhf (2.4.8-1) ...
Selecting previously unselected package libjsoncpp25:armhf.
Preparing to unpack .../29-libjsoncpp25_1.9.5-4_armhf.deb ...
Unpacking libjsoncpp25:armhf (1.9.5-4) ...
Selecting previously unselected package librhash0:armhf.
Preparing to unpack .../30-librhash0_1.4.2-1_armhf.deb ...
Unpacking librhash0:armhf (1.4.2-1) ...
Selecting previously unselected package libuv1:armhf.
Preparing to unpack .../31-libuv1_1.44.1-2+rpi1_armhf.deb ...
Unpacking libuv1:armhf (1.44.1-2+rpi1) ...
Selecting previously unselected package dh-elpa-helper.
Preparing to unpack .../32-dh-elpa-helper_2.0.10_all.deb ...
Unpacking dh-elpa-helper (2.0.10) ...
Selecting previously unselected package emacsen-common.
Preparing to unpack .../33-emacsen-common_3.0.4_all.deb ...
Unpacking emacsen-common (3.0.4) ...
Selecting previously unselected package cmake-data.
Preparing to unpack .../34-cmake-data_3.23.2-1_all.deb ...
Unpacking cmake-data (3.23.2-1) ...
Selecting previously unselected package cmake.
Preparing to unpack .../35-cmake_3.23.2-1_armhf.deb ...
Unpacking cmake (3.23.2-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../36-libdebhelper-perl_13.7.1_all.deb ...
Unpacking libdebhelper-perl (13.7.1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../37-libtool_2.4.7-4_all.deb ...
Unpacking libtool (2.4.7-4) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../38-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../39-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../40-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../41-libfile-stripnondeterminism-perl_1.13.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../42-dh-strip-nondeterminism_1.13.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../43-libelf1_0.187-1_armhf.deb ...
Unpacking libelf1:armhf (0.187-1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../44-dwz_0.14-1_armhf.deb ...
Unpacking dwz (0.14-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../45-gettext_0.21-6_armhf.deb ...
Unpacking gettext (0.21-6) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../46-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../47-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../48-debhelper_13.7.1_all.deb ...
Unpacking debhelper (13.7.1) ...
Selecting previously unselected package hdf5-helpers.
Preparing to unpack .../49-hdf5-helpers_1.10.7+repack-4+rpi1+b1_armhf.deb ...
Unpacking hdf5-helpers (1.10.7+repack-4+rpi1+b1) ...
Selecting previously unselected package libaec0:armhf.
Preparing to unpack .../50-libaec0_1.0.6-1_armhf.deb ...
Unpacking libaec0:armhf (1.0.6-1) ...
Selecting previously unselected package libsz2:armhf.
Preparing to unpack .../51-libsz2_1.0.6-1_armhf.deb ...
Unpacking libsz2:armhf (1.0.6-1) ...
Selecting previously unselected package libaec-dev:armhf.
Preparing to unpack .../52-libaec-dev_1.0.6-1_armhf.deb ...
Unpacking libaec-dev:armhf (1.0.6-1) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../53-libblas3_3.10.1-2_armhf.deb ...
Unpacking libblas3:armhf (3.10.1-2) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../54-libgfortran5_12.1.0-2+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (12.1.0-2+rpi1) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../55-liblapack3_3.10.1-2_armhf.deb ...
Unpacking liblapack3:armhf (3.10.1-2) ...
Selecting previously unselected package libarpack2:armhf.
Preparing to unpack .../56-libarpack2_3.8.0-1_armhf.deb ...
Unpacking libarpack2:armhf (3.8.0-1) ...
Selecting previously unselected package libsuperlu5:armhf.
Preparing to unpack .../57-libsuperlu5_5.3.0+dfsg1-2_armhf.deb ...
Unpacking libsuperlu5:armhf (5.3.0+dfsg1-2) ...
Selecting previously unselected package libarmadillo11.
Preparing to unpack .../58-libarmadillo11_1%3a11.1.1+dfsg-3_armhf.deb ...
Unpacking libarmadillo11 (1:11.1.1+dfsg-3) ...
Selecting previously unselected package libblas-dev:armhf.
Preparing to unpack .../59-libblas-dev_3.10.1-2_armhf.deb ...
Unpacking libblas-dev:armhf (3.10.1-2) ...
Selecting previously unselected package liblapack-dev:armhf.
Preparing to unpack .../60-liblapack-dev_3.10.1-2_armhf.deb ...
Unpacking liblapack-dev:armhf (3.10.1-2) ...
Selecting previously unselected package libarpack2-dev:armhf.
Preparing to unpack .../61-libarpack2-dev_3.8.0-1_armhf.deb ...
Unpacking libarpack2-dev:armhf (3.8.0-1) ...
Selecting previously unselected package libhdf5-103-1:armhf.
Preparing to unpack .../62-libhdf5-103-1_1.10.7+repack-4+rpi1+b1_armhf.deb ...
Unpacking libhdf5-103-1:armhf (1.10.7+repack-4+rpi1+b1) ...
Selecting previously unselected package libhdf5-fortran-102:armhf.
Preparing to unpack .../63-libhdf5-fortran-102_1.10.7+repack-4+rpi1+b1_armhf.deb ...
Unpacking libhdf5-fortran-102:armhf (1.10.7+repack-4+rpi1+b1) ...
Selecting previously unselected package libhdf5-hl-100:armhf.
Preparing to unpack .../64-libhdf5-hl-100_1.10.7+repack-4+rpi1+b1_armhf.deb ...
Unpacking libhdf5-hl-100:armhf (1.10.7+repack-4+rpi1+b1) ...
Selecting previously unselected package libhdf5-hl-fortran-100:armhf.
Preparing to unpack .../65-libhdf5-hl-fortran-100_1.10.7+repack-4+rpi1+b1_armhf.deb ...
Unpacking libhdf5-hl-fortran-100:armhf (1.10.7+repack-4+rpi1+b1) ...
Selecting previously unselected package libhdf5-cpp-103-1:armhf.
Preparing to unpack .../66-libhdf5-cpp-103-1_1.10.7+repack-4+rpi1+b1_armhf.deb ...
Unpacking libhdf5-cpp-103-1:armhf (1.10.7+repack-4+rpi1+b1) ...
Selecting previously unselected package libhdf5-hl-cpp-100:armhf.
Preparing to unpack .../67-libhdf5-hl-cpp-100_1.10.7+repack-4+rpi1+b1_armhf.deb ...
Unpacking libhdf5-hl-cpp-100:armhf (1.10.7+repack-4+rpi1+b1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../68-zlib1g-dev_1%3a1.2.11.dfsg-4+b2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-4+b2) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../69-libjpeg62-turbo_1%3a2.1.2-1_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:2.1.2-1) ...
Selecting previously unselected package libjpeg62-turbo-dev:armhf.
Preparing to unpack .../70-libjpeg62-turbo-dev_1%3a2.1.2-1_armhf.deb ...
Unpacking libjpeg62-turbo-dev:armhf (1:2.1.2-1) ...
Selecting previously unselected package libjpeg-dev:armhf.
Preparing to unpack .../71-libjpeg-dev_1%3a2.1.2-1_armhf.deb ...
Unpacking libjpeg-dev:armhf (1:2.1.2-1) ...
Selecting previously unselected package libcurl4-openssl-dev:armhf.
Preparing to unpack .../72-libcurl4-openssl-dev_7.83.1-2_armhf.deb ...
Unpacking libcurl4-openssl-dev:armhf (7.83.1-2) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../73-libssl-dev_3.0.3-7_armhf.deb ...
Unpacking libssl-dev:armhf (3.0.3-7) ...
Selecting previously unselected package libhdf5-dev.
Preparing to unpack .../74-libhdf5-dev_1.10.7+repack-4+rpi1+b1_armhf.deb ...
Unpacking libhdf5-dev (1.10.7+repack-4+rpi1+b1) ...
Selecting previously unselected package libsuperlu-dev:armhf.
Preparing to unpack .../75-libsuperlu-dev_5.3.0+dfsg1-2_armhf.deb ...
Unpacking libsuperlu-dev:armhf (5.3.0+dfsg1-2) ...
Selecting previously unselected package libarmadillo-dev.
Preparing to unpack .../76-libarmadillo-dev_1%3a11.1.1+dfsg-3_armhf.deb ...
Unpacking libarmadillo-dev (1:11.1.1+dfsg-3) ...
Selecting previously unselected package libbamtools2.5.1:armhf.
Preparing to unpack .../77-libbamtools2.5.1_2.5.1+dfsg-10+b1_armhf.deb ...
Unpacking libbamtools2.5.1:armhf (2.5.1+dfsg-10+b1) ...
Selecting previously unselected package libbamtools-dev:armhf.
Preparing to unpack .../78-libbamtools-dev_2.5.1+dfsg-10+b1_armhf.deb ...
Unpacking libbamtools-dev:armhf (2.5.1+dfsg-10+b1) ...
Selecting previously unselected package libboost1.74-dev:armhf.
Preparing to unpack .../79-libboost1.74-dev_1.74.0-16_armhf.deb ...
Unpacking libboost1.74-dev:armhf (1.74.0-16) ...
Selecting previously unselected package libboost-math1.74.0:armhf.
Preparing to unpack .../80-libboost-math1.74.0_1.74.0-16_armhf.deb ...
Unpacking libboost-math1.74.0:armhf (1.74.0-16) ...
Selecting previously unselected package libboost-math1.74-dev:armhf.
Preparing to unpack .../81-libboost-math1.74-dev_1.74.0-16_armhf.deb ...
Unpacking libboost-math1.74-dev:armhf (1.74.0-16) ...
Selecting previously unselected package libboost-math-dev:armhf.
Preparing to unpack .../82-libboost-math-dev_1.74.0.3+b4_armhf.deb ...
Unpacking libboost-math-dev:armhf (1.74.0.3+b4) ...
Selecting previously unselected package libdisorder0:armhf.
Preparing to unpack .../83-libdisorder0_0.0.2+git20130809.8062ee1-4_armhf.deb ...
Unpacking libdisorder0:armhf (0.0.2+git20130809.8062ee1-4) ...
Selecting previously unselected package libdisorder-dev:armhf.
Preparing to unpack .../84-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 .../85-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 .../86-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 .../87-libsmithwaterman-dev_0.0+git20160702.2610e25-12_armhf.deb ...
Unpacking libsmithwaterman-dev:armhf (0.0+git20160702.2610e25-12) ...
Selecting previously unselected package sbuild-build-depends-tvc-dummy.
Preparing to unpack .../88-sbuild-build-depends-tvc-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-tvc-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.4.8-1) ...
Setting up libpipeline1:armhf (1.5.6-1) ...
Setting up libdisorder0:armhf (0.0.2+git20130809.8062ee1-4) ...
Setting up libicu71:armhf (71.1-3) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up libboost1.74-dev:armhf (1.74.0-16) ...
Setting up bsdextrautils (2.38-4) ...
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 libdebhelper-perl (13.7.1) ...
Setting up libbrotli1:armhf (1.0.9-2+b2) ...
Setting up libsmithwaterman0:armhf (0.0+git20160702.2610e25-12) ...
Setting up libnghttp2-14:armhf (1.47.0-1+b1) ...
Setting up libmagic1:armhf (1:5.41-4) ...
Setting up gettext-base (0.21-6) ...
Setting up file (1:5.41-4) ...
Setting up libgomp1:armhf (12.1.0-2+rpi1) ...
Setting up libaec0:armhf (1.0.6-1) ...
Setting up autotools-dev (20220109.1) ...
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 libsigsegv2:armhf (2.14-1) ...
Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-10+b1) ...
Setting up libatomic1:armhf (12.1.0-2+rpi1) ...
Setting up autopoint (0.21-6) ...
Setting up libjsoncpp25:armhf (1.9.5-4) ...
Setting up libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-4) ...
Setting up libgfortran5:armhf (12.1.0-2+rpi1) ...
Setting up libboost-math1.74.0:armhf (1.74.0-16) ...
Setting up libubsan1:armhf (12.1.0-2+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-4+b2) ...
Setting up librhash0:armhf (1.4.2-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up sgml-base (1.30) ...
Setting up cmake-data (3.23.2-1) ...
Setting up libboost-math1.74-dev:armhf (1.74.0-16) ...
Setting up libelf1:armhf (0.187-1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1) ...
Setting up libcc1-0:armhf (12.1.0-2+rpi1) ...
Setting up libprocps8:armhf (2:3.3.17-7) ...
Setting up libsz2:armhf (1.0.6-1) ...
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up libjsoncpp-dev:armhf (1.9.5-4) ...
Setting up gettext (0.21-6) ...
Setting up libtool (2.4.7-4) ...
Setting up libarchive13:armhf (3.6.0-1) ...
Setting up libboost-math-dev:armhf (1.74.0.3+b4) ...
Setting up libaec-dev:armhf (1.0.6-1) ...
Setting up libssl3:armhf (3.0.3-7) ...
Setting up libjpeg-dev:armhf (1:2.1.2-1) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
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 libbamtools-dev:armhf (2.5.1+dfsg-10+b1) ...
Setting up libssl-dev:armhf (3.0.3-7) ...
Setting up libsmithwaterman-dev:armhf (0.0+git20160702.2610e25-12) ...
Setting up autoconf (2.71-2) ...
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 libssh2-1:armhf (1.10.0-3+b1) ...
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 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 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 po-debconf (1.0.21+nmu1) ...
Setting up libarpack2:armhf (3.8.0-1) ...
Setting up libsuperlu5:armhf (5.3.0+dfsg1-2) ...
Setting up man-db (2.10.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
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 libcurl4:armhf (7.83.1-2) ...
Setting up libsuperlu-dev:armhf (5.3.0+dfsg1-2) ...
Setting up libarpack2-dev:armhf (3.8.0-1) ...
Setting up libarmadillo11 (1:11.1.1+dfsg-3) ...
Setting up debhelper (13.7.1) ...
Setting up libcurl4-openssl-dev:armhf (7.83.1-2) ...
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 (3.23.2-1) ...
Setting up libhdf5-hl-100:armhf (1.10.7+repack-4+rpi1+b1) ...
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 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 (1:11.1.1+dfsg-3) ...
Setting up sbuild-build-depends-tvc-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.33-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-163-generic armhf (armv8l)
Toolchain package versions: binutils_2.38-3+rpi1 dpkg-dev_1.21.7+rpi1 g++-11_11.2.0-20+rpi1 gcc-11_11.2.0-20+rpi1 libc6-dev_2.33-7+rpi1 libstdc++-11-dev_11.2.0-20+rpi1 libstdc++6_12.1.0-2+rpi1 linux-libc-dev_5.16.18-1+rpi1
Package versions: adduser_3.121 apt_2.4.5 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.5.52 bash_5.1-6 binutils_2.38-3+rpi1 binutils-arm-linux-gnueabihf_2.38-3+rpi1 binutils-common_2.38-3+rpi1 bsdextrautils_2.38-4 bsdutils_1:2.38-4 build-essential_12.9 bzip2_1.0.8-5 cmake_3.23.2-1 cmake-data_3.23.2-1 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-20+rpi1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.7.1 debianutils_5.7-0.1 dh-autoreconf_20 dh-elpa-helper_2.0.10 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-3+b1 dpkg_1.21.7+rpi1 dpkg-dev_1.21.7+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 emacsen-common_3.0.4 fakeroot_1.28-1 file_1:5.41-4 findutils_4.9.0-2 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-20+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-20+rpi1 gcc-11-base_11.2.0-20+rpi1 gcc-12-base_12.1.0-2+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_0.21-6 gettext-base_0.21-6 gnupg_2.2.27-3 gnupg-l10n_2.2.27-3 gnupg-utils_2.2.27-3+b1 gpg_2.2.27-3+b1 gpg-agent_2.2.27-3+b1 gpg-wks-client_2.2.27-3+b1 gpg-wks-server_2.2.27-3+b1 gpgconf_2.2.27-3+b1 gpgsm_2.2.27-3+b1 gpgv_2.2.27-3+b1 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_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapt-pkg6.0_2.4.5 libarchive-zip-perl_1.68-1 libarchive13_3.6.0-1 libarmadillo-dev_1:11.1.1+dfsg-3 libarmadillo11_1:11.1.1+dfsg-3 libarpack2_3.8.0-1 libarpack2-dev_3.8.0-1 libasan6_11.2.0-20+rpi1 libassuan0_2.5.5-1 libatomic1_12.1.0-2+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbamtools-dev_2.5.1+dfsg-10+b1 libbamtools2.5.1_2.5.1+dfsg-10+b1 libbinutils_2.38-3+rpi1 libblas-dev_3.10.1-2 libblas3_3.10.1-2 libblkid1_2.38-4 libboost-math-dev_1.74.0.3+b4 libboost-math1.74-dev_1.74.0-16 libboost-math1.74.0_1.74.0-16 libboost1.74-dev_1.74.0-16 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5 libc-bin_2.33-7+rpi1 libc-dev-bin_2.33-7+rpi1 libc6_2.33-7+rpi1 libc6-dev_2.33-7+rpi1 libcap-ng0_0.7.9-2.2+b2 libcap2_1:2.44-1 libcc1-0_12.1.0-2+rpi1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.38-3+rpi1 libctf0_2.38-3+rpi1 libcurl4_7.83.1-2 libcurl4-openssl-dev_7.83.1-2 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.262 libdebhelper-perl_13.7.1 libdisorder-dev_0.0.2+git20130809.8062ee1-4 libdisorder0_0.0.2+git20130809.8062ee1-4 libdpkg-perl_1.21.7+rpi1 libelf1_0.187-1 libexpat1_2.4.8-1 libext2fs2_1.46.5-2 libfakeroot_1.28-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.2.0-20+rpi1 libgcc-s1_12.1.0-2+rpi1 libgcrypt20_1.10.1-2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgfortran5_12.1.0-2+rpi1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.4-2 libgomp1_12.1.0-2+rpi1 libgpg-error0_1.43-3 libgssapi-krb5-2_1.19.2-2+b2 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_3.7.3-1 libicu71_71.1-3 libidn2-0_2.3.2-2 libisl23_0.24-2 libjpeg-dev_1:2.1.2-1 libjpeg62-turbo_1:2.1.2-1 libjpeg62-turbo-dev_1:2.1.2-1 libjsoncpp-dev_1.9.5-4 libjsoncpp25_1.9.5-4 libk5crypto3_1.19.2-2+b2 libkeyutils1_1.6.1-3+rpi1 libkrb5-3_1.19.2-2+b2 libkrb5support0_1.19.2-2+b2 libksba8_1.6.0-2 liblapack-dev_3.10.1-2 liblapack3_3.10.1-2 libldap-2.5-0_2.5.11+dfsg-1+rpi1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38-4 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.7.3-1 libnghttp2-14_1.47.0-1+b1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-4 libpcre3_2:8.39-14 libperl5.34_5.34.0-4 libpipeline1_1.5.6-1 libprocps8_2:3.3.17-7 libpsl5_0.21.0-1.2 libreadline8_8.1.2-1.2 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-4 libsasl2-modules-db_2.1.28+dfsg-4 libseccomp2_2.5.3-2+rpi1+b1 libselinux1_3.3-1+b1 libsemanage-common_3.3-1 libsemanage2_3.3-1+b1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.14-1 libsmartcols1_2.38-4 libsmithwaterman-dev_0.0+git20160702.2610e25-12 libsmithwaterman0_0.0+git20160702.2610e25-12 libsqlite3-0_3.38.2-1 libss2_1.46.5-2 libssh2-1_1.10.0-3+b1 libssl-dev_3.0.3-7 libssl1.1_1.1.1n-1 libssl3_3.0.3-7 libstdc++-11-dev_11.2.0-20+rpi1 libstdc++6_12.1.0-2+rpi1 libsub-override-perl_0.09-2 libsuperlu-dev_5.3.0+dfsg1-2 libsuperlu5_5.3.0+dfsg1-2 libsystemd0_250.4-1+rpi1 libsz2_1.0.6-1 libtasn1-6_4.18.0-4 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.7-4 libubsan1_12.1.0-2+rpi1 libuchardet0_0.0.7-1 libudev1_250.4-1+rpi1 libunistring2_1.0-1 libuuid1_2.38-4 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_5.16.18-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3 mount_2.38-4 ncurses-base_6.3-2 ncurses-bin_6.3-2 netbase_6.3 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-4 perl-base_5.34.0-4 perl-modules-5.34_5.34.0-4 pinentry-curses_1.1.0-4 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-core-dummy_0.invalid.0 sbuild-build-depends-tvc-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 sysvinit-utils_3.03-1 tar_1.34+dfsg-1 tzdata_2022a-1 util-linux_2.37.3-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4+b2 zlib1g-dev_1:1.2.11.dfsg-4+b2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.TewzVGjr/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 /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg
dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz
dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying cmake.patch
dpkg-source: info: applying bamtools.patch
dpkg-source: info: applying help.patch
dpkg-source: info: applying hurd.patch
dpkg-source: info: applying sse.patch
dpkg-source: info: applying use_debian_packaged_smithwaterman.patch
dpkg-source: info: applying python3.patch
dpkg-source: info: applying gcc11.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 5.0.3+git20151221.80e144e+dfsg-4+b2
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-57a27077-f4af-4c33-8e5d-a918334280dc
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package tvc
dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-4+b2
dpkg-buildpackage: info: source distribution bookworm-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf ..
CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
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 11.2.0
-- The CXX compiler identification is GNU 11.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- CMAKE_CXX_FLAGS: '-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -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
-- Build files have been written to: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/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 '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -B/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/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 '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/tvcutils.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/tvc.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build
make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
[ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o
[ 3%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o
[ 4%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/tvcutils.cpp
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/IndelAssembly/IndelAssembly.cpp
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp
[ 6%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp
[ 7%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/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 /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/prepare_hotspots.cpp
[ 9%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/BAMWalkerEngine.cpp
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:9: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations]
36 | arma::set_stream_err1(null_ostream);
| ^~~~~~~~~~~~~~~
In file included from /usr/include/armadillo:358,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:92:1: note: declared here
92 | set_stream_err1(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations]
36 | arma::set_stream_err1(null_ostream);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/armadillo:358,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:92:1: note: declared here
92 | set_stream_err1(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:9: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations]
37 | arma::set_stream_err2(null_ostream);
| ^~~~~~~~~~~~~~~
In file included from /usr/include/armadillo:358,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:103:1: note: declared here
103 | set_stream_err2(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations]
37 | arma::set_stream_err2(null_ostream);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/armadillo:358,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:103:1: note: declared here
103 | set_stream_err2(std::ostream& user_stream)
| ^~~~~~~~~~~~~~~
[ 10%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/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 /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/validate_bed.cpp
[ 12%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp
[ 14%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp
[ 15%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o -MF CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o.d -o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp
[ 17%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/OrderedBAMWriter.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 18%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp
[ 20%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -MF CMakeFiles/tvcassembly.dir/IonVersion.cpp.o.d -o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/IonVersion.cpp
[ 21%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp
[ 23%] Linking CXX executable tvcassembly
/usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -o tvcassembly -lbamtools -lz -lpthread -ljsoncpp
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
[ 23%] Built target tvcassembly
[ 25%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HandleVariant.cpp
[ 26%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HotspotReader.cpp
[ 28%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp
[ 29%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/MetricsManager.cpp
[ 31%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp
[ 32%] Building CXX object CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 34%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/MiscUtil.cpp
[ 35%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp
[ 37%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp
[ 39%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/ExtendParameters.cpp
[ 40%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:13:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator<markov_state>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<markov_state>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator<markov_state>]':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<markov_state*, std::vector<markov_state> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void markov_chain<T>::generate_states(T, T) [with T = unsigned int]':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<markov_state*, std::vector<markov_state> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 42%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/VcfFormat.cpp
[ 43%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:12,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DPTreephaser&}; _Tp = DPTreephaser; _Alloc = std::allocator<DPTreephaser>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<DPTreephaser>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:12,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7:
/usr/include/c++/11/bits/stl_vector.h: In constructor 'PersistingThreadObjects::PersistingThreadObjects(const InputStructures&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DPTreephaser*, std::vector<DPTreephaser> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 45%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads/ExtendedReadInfo.cpp
[ 46%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function 'ti_index_core':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow]
336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
| ^~~~~~~~
[ 48%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ErrorMotifs.cpp
[ 50%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
678 | fread(buf, 1, 28, fp->file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 51%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/LocalContext.cpp
[ 53%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/IonVersion.cpp.o -MF CMakeFiles/tvcutils.dir/IonVersion.cpp.o.d -o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/IonVersion.cpp
[ 54%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ClassifyVariant.cpp
[ 56%] 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=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/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 '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
[ 56%] Built target tvcutils
[ 57%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/SpliceVariantHypotheses.cpp
[ 59%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/DecisionTreeData.cpp
[ 60%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector<float>&, std::vector<float>&, bool)':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:191:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<float>::size_type' {aka 'unsigned int'} [-Wformat=]
191 | fprintf(stdout, "ref.size()=%lu; ", ref.size());
| ~~^ ~~~~~~~~~~
| | |
| | std::vector<float>::size_type {aka unsigned int}
| long unsigned int
| %u
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:192:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<float>::size_type' {aka 'unsigned int'} [-Wformat=]
192 | fprintf(stdout, "var.size()=%lu; ", var.size());
| ~~^ ~~~~~~~~~~
| | |
| | std::vector<float>::size_type {aka unsigned int}
| long unsigned int
| %u
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:193:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wformat=]
193 | fprintf(stdout, "both.size()=%lu; ", both.size());
| ~~^ ~~~~~~~~~~~
| | |
| | std::vector<double>::size_type {aka unsigned int}
| long unsigned int
| %u
[ 62%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HypothesisEvaluator.cpp
[ 64%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/DiagnosticJSON.cpp
[ 65%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/BiasGenerator.cpp
[ 67%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/SigmaGenerator.cpp
[ 68%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/SkewGenerator.cpp
[ 70%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/PosteriorInference.cpp
[ 71%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/ShortStack.cpp
[ 73%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/StackEngine.cpp
[ 75%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/CrossHypotheses.cpp
[ 76%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp
[ 78%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/split.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/split.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp
[ 79%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp
[ 81%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function 'ti_index_core':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow]
336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
| ^~~~~~~~
[ 82%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
678 | fread(buf, 1, 28, fp->file);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 84%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -MF CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o.d -o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src/AlleleParser.cpp
[ 85%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/PIDloop.cpp
[ 87%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/DPTreephaser.cpp
[ 89%] Building CXX object CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -MF CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o.d -o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.cpp
[ 90%] Building CXX object CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o -MF CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o.d -o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/FlowAlignment.cpp
[ 92%] Building CXX object CMakeFiles/tvc.dir/Util/OptArgs.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvc.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp
[ 93%] Building CXX object CMakeFiles/tvc.dir/realignment/Realigner.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/realignment/Realigner.cpp.o -MF CMakeFiles/tvc.dir/realignment/Realigner.cpp.o.d -o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment/Realigner.cpp
[ 95%] Building C object CMakeFiles/tvc.dir/file-io/ion_util.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/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 /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io/ion_util.c
[ 96%] Building C object CMakeFiles/tvc.dir/file-io/ion_error.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/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 /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io/ion_error.c
[ 98%] Building CXX object CMakeFiles/tvc.dir/IonVersion.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/IonVersion.cpp.o -MF CMakeFiles/tvc.dir/IonVersion.cpp.o.d -o CMakeFiles/tvc.dir/IonVersion.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/IonVersion.cpp
In file included from /usr/include/c++/11/vector:72,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11,
from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/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 '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
[100%] Built target tvc
make[2]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0
make[1]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
dh_auto_test -a
cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=--verbose ARGS\+=-j4
make[1]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
Running tests...
/usr/bin/ctest --force-new-ctest-process --verbose -j4
UpdateCTestConfiguration from :/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl
Test project /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: tvc_call
1: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc
1: Test timeout computed to be: 10000000
test 2
Start 2: tvc_test_1_thread_sse_off
2: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc "--input-bam" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/test1" "--output-vcf" "small_variants.vcf"
2: Test timeout computed to be: 10000000
test 3
Start 3: tvc_test_4_threads_sse_off_with_parameter_file
3: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc "--input-bam" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/test2" "--output-vcf" "small_variants.vcf"
3: Test timeout computed to be: 10000000
test 4
Start 4: tvcutils_call
4: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils
4: Test timeout computed to be: 10000000
1: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
1:
1: Usage: tvc [options]
1:
1: General options:
1: -h,--help print this help message and exit
1: -v,--version print version and exit
1: -n,--num-threads INT number of worker threads [2]
1: -N,--num-variants-per-thread INT worker thread batch size [500]
1: --parameters-file FILE json file with algorithm control parameters [optional]
1:
1: Inputs:
1: -r,--reference FILE reference fasta file [required]
1: -b,--input-bam FILE bam file with mapped reads [required]
1: -g,--sample-name STRING sample for which variants are called (In case of input BAM files with multiple samples) [optional if there is only one sample]
1: --force-sample-name STRING force all read groups to have this sample name [off]
1: -t,--target-file FILE only process targets in this bed file [optional]
1: --trim-ampliseq-primers on/off match reads to targets and trim the ends that reach outside them [off]
1: -D,--downsample-to-coverage INT ?? [2000]
1: --model-file FILE HP recalibration model input file.
1: --recal-model-hp-thres INT Lower threshold for HP recalibration.
1:
1: Outputs:
1: -O,--output-dir DIRECTORY base directory for all output files [current dir]
1: -o,--output-vcf FILE vcf file with variant calling results [required]
1: --suppress-reference-genotypes on/off write reference calls into the filtered variants vcf [on]
1: --suppress-no-calls on/off write filtered variants into the filtered variants vcf [on]
1: --suppress-nocall-genotypes on/off do not report a genotype for filtered variants [on]
1:
1: Variant candidate generation (FreeBayes):
1: --allow-snps on/off allow generation of snp candidates [on]
1: --allow-indels on/off allow generation of indel candidates [on]
1: --allow-mnps on/off allow generation of mnp candidates [on]
1: --allow-complex on/off allow generation of block substitution candidates [off]
1: --max-complex-gap INT maximum number of reference alleles between two alternate alleles to allow merging of the alternate alleles [1]
1: -m,--use-best-n-alleles INT maximum number of snp alleles [2]
1: -M,--min-mapping-qv INT do not use reads with mapping quality below this [4]
1: -U,--read-snp-limit INT do not use reads with number of snps above this [10]
1: -z,--read-max-mismatch-fraction FLOAT do not use reads with fraction of mismatches above this [1.0]
1: --gen-min-alt-allele-freq FLOAT minimum required alt allele frequency to generate a candidate [0.2]
1: --gen-min-indel-alt-allele-freq FLOAT minimum required alt allele frequency to generate a homopolymer indel candidate [0.2]
1: --gen-min-coverage INT minimum required coverage to generate a candidate [6]
1:
1: External variant candidates:
1: -c,--input-vcf FILE vcf.gz file (+.tbi) with additional candidate variant locations and alleles [optional]
1: --process-input-positions-only on/off only generate candidates at locations from input-vcf [off]
1: --use-input-allele-only on/off only consider provided alleles for locations in input-vcf [off]
1:
1: Variant candidate scoring options:
1: --min-delta-for-flow FLOAT minimum prediction delta for scoring flows [0.1]
1: --max-flows-to-test INT maximum number of scoring flows [10]
1: --outlier-probability FLOAT probability for outlier reads [0.01]
1: --heavy-tailed INT degrees of freedom in t-dist modeling signal residual heavy tail [3]
1: --suppress-recalibration on/off Suppress homopolymer recalibration [on].
1: --do-snp-realignment on/off Realign reads in the vicinity of candidate snp variants [on].
1: --do-mnp-realignment on/off Realign reads in the vicinity of candidate mnp variants [do-snp-realignment].
1: --realignment-threshold FLOAT Max. allowed fraction of reads where realignment causes an alignment change [1.0].
1:
1: Advanced variant candidate scoring options:
1: --use-sse-basecaller on/off Switch to use the vectorized version of the basecaller [off].
1: --resolve-clipped-bases on/off If 'true', the basecaller is used to solve soft clipped bases [off].
1: --prediction-precision FLOAT prior weight in bias estimator [30.0]
1: --shift-likelihood-penalty FLOAT penalize log-likelihood for solutions involving large systematic bias [0.3]
1: --minimum-sigma-prior FLOAT prior variance per data point, constant [0.085]
1: --slope-sigma-prior FLOAT prior rate of increase of variance over minimum by signal [0.0084]
1: --sigma-prior-weight FLOAT weight of prior estimate of variance compared to observations [1.0]
1: --k-zero FLOAT variance increase for adding systematic bias [3.0]
1: --sse-relative-safety-level FLOAT dampen strand bias detection for SSE events for low coverage [0.025]
1: --tune-sbias FLOAT dampen strand bias detection for low coverage [0.01]
1: --max-detail-level INT number of evaluated frequencies for a given hypothesis, reduce for very high coverage, set to zero to disable this option [0]
1:
1: Variant filtering:
1: -k,--snp-min-coverage INT filter out snps with total coverage below this [6]
1: -C,--snp-min-cov-each-strand INT filter out snps with coverage on either strand below this [0]
1: -B,--snp-min-variant-score FLOAT filter out snps with QUAL score below this [10.0]
1: -s,--snp-strand-bias FLOAT filter out snps with strand bias above this [0.95] given pval < snp-strand-bias-pval
1: --snp-strand-bias-pval FLOAT filter out snps with pval below this [1.0] given strand bias > snp-strand-bias
1: -A,--snp-min-allele-freq FLOAT minimum required alt allele frequency for non-reference snp calls [0.2]
1: --mnp-min-coverage INT filter out mnps with total coverage below this [snp-min-coverage]
1: --mnp-min-cov-each-strand INT filter out mnps with coverage on either strand below this, [snp-min-cov-each-strand]
1: --mnp-min-variant-score FLOAT filter out mnps with QUAL score below this [snp-min-variant-score]
1: --mnp-strand-bias FLOAT filter out mnps with strand bias above this [snp-strand-bias] given pval < mnp-strand-bias-pval
1: --mnp-strand-bias-pval FLOAT filter out mnps with pval below this [snp-strand-bias-pval] given strand bias > mnp-strand-bias
1: --mnp-min-allele-freq FLOAT minimum required alt allele frequency for non-reference mnp calls [snp-min-allele-freq]
1: --indel-min-coverage INT filter out indels with total coverage below this [30]
1: --indel-min-cov-each-strand INT filter out indels with coverage on either strand below this [1]
1: --indel-min-variant-score FLOAT filter out indels with QUAL score below this [10.0]
1: -S,--indel-strand-bias FLOAT filter out indels with strand bias above this [0.95] given pval < indel-strand-bias-pval
1: --indel-strand-bias-pval FLOAT filter out indels with pval below this [1.0] given strand bias > indel-strand-bias
1: --indel-min-allele-freq FLOAT minimum required alt allele frequency for non-reference indel call [0.2]
1: --hotspot-min-coverage INT filter out hotspot variants with total coverage below this [6]
1: --hotspot-min-cov-each-strand INT filter out hotspot variants with coverage on either strand below this [snp-min-cov-each-strand]
1: --hotspot-min-variant-score FLOAT filter out hotspot variants with QUAL score below this [snp-min-variant-score]
1: --hotspot-strand-bias FLOAT filter out hotspot variants with strand bias above this [0.95] given pval < hotspot-strand-bias-pval
1: --hotspot-strand-bias-pval FLOAT filter out hotspot variants with pval below this [1.0] given strand bias > hotspot-strand-bias
1: -H,--hotspot-min-allele-freq FLOAT minimum required alt allele frequency for non-reference hotspot variant call [0.2]
1: -L,--hp-max-length INT filter out indels in homopolymers above this [8]
1: -e,--error-motifs FILE table of systematic error motifs and their error rates [optional]
1: --sse-prob-threshold FLOAT filter out variants in motifs with error rates above this [0.2]
1: --min-ratio-reads-non-sse-strand FLOAT minimum required alt allele frequency for variants with error motifs on opposite strand [0.2]
1: --indel-as-hpindel on/off apply indel filters to non HP indels [off]
1:
1: Position bias variant filtering:
1: --use-position-bias on/off enable the position bias filter [off]
1: --position-bias FLOAT filter out variants with position bias relative to soft clip ends in reads > position-bias [0.75]
1: --position-bias-pval FLOAT filter out if position bias above position-bias given pval < position-bias-pval [0.05]
1: --position-bias-ref-fraction FLOAT skip position bias filter if (reference read count)/(reference + alt allele read count) <= to this [0.05]
1:
1: Filters that depend on scoring across alleles:
1: --data-quality-stringency FLOAT minimum mean log-likelihood delta per read [4.0]
1: --read-rejection-threshold FLOAT filter variants where large numbers of reads are rejected as outliers [0.5]
1: --filter-unusual-predictions FLOAT posterior log likelihood threshold for accepting bias estimate [0.3]
1: --filter-deletion-predictions FLOAT check post-evaluation systematic bias in deletions; a high value like 100 effectively turns off this filter [100.0]
1: --filter-insertion-predictions FLOAT check post-evaluation systematic bias in insertions; a high value like 100 effectively turns off this filter [100.0]
1:
1: --heal-snps on/off suppress in/dels not participating in diploid variant genotypes if the genotype contains a SNP or MNP [on].
1:
1: Debugging:
1: -d,--debug INT (0/1/2) display extra debug messages [0]
1: --do-json-diagnostic on/off (devel) dump internal state to json file (uses much more time/memory/disk) [off]
1: --postprocessed-bam FILE (devel) save tvc-processed reads to an (unsorted) BAM file [optional]
1: --do-minimal-diagnostic on/off (devel) provide minimal read information for called variants [off]
1: --override-limits on/off (devel) disable limit-check on input parameters [off].
1:
2: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
2:
2: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf
2: hp-max-length = 8 (integer, builtin default)
2: sse-prob-threshold = 0.2 (double, builtin default)
2: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default)
2: sse-relative-safety-level = 0.025 (double, builtin default)
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)
1/8 Test #1: tvc_call ......................................... Passed 0.01 sec
test 5
Start 5: tvcutils_prepare_hotspots_call
5: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "prepare_hotspots"
5: Test timeout computed to be: 10000000
2: 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 /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed
2: TargetsManager: 1 target(s)
2: TargetsManager: Trimming of AmpliSeq primers is enabled
4:
4: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
4:
4: Usage: tvcutils <command> [options]
4:
4: Commands:
4: prepare_hotspots Convert BED or VCF file into a valid hotspot file
4: validate_bed Validate targets or hotspots file
4: unify_vcf Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots)
4:
3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
3:
3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf
3: hp-max-length = 8 (integer, parameters json file)
3: sse-prob-threshold = 1 (double, parameters json file)
3: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default)
3: sse-relative-safety-level = 0.025 (double, builtin default)
3: do-snp-realignment = false (boolean, parameters json file)
3: do-mnp-realignment = false (boolean, parameters json file)
3: realignment-threshold = 0 (double, parameters json file)
3: indel-as-hpindel = false (boolean, parameters json file)
3: data-quality-stringency = 10 (double, parameters json file)
3: read-rejection-threshold = 0.5 (double, builtin default)
3: use-position-bias = false (boolean, parameters json file)
3: position-bias-ref-fraction = 0.05 (double, parameters json file)
3: position-bias = 0.75 (double, parameters json file)
3: position-bias-pval = 0.05 (double, parameters json file)
3: downsample-to-coverage = 2000 (integer, parameters json file)
3: tune-sbias = 0.01 (double, builtin default)
3: suppress-reference-genotypes = true (boolean, builtin default)
3: suppress-nocall-genotypes = true (boolean, builtin default)
3: suppress-no-calls = true (boolean, builtin default)
3: heal-snps = true (boolean, builtin default)
3: snp-min-cov-each-strand = 4 (integer, parameters json file)
3: snp-min-variant-score = 6 (double, parameters json file)
3: snp-min-allele-freq = 0.02 (double, parameters json file)
3: snp-min-coverage = 100 (integer, parameters json file)
3: snp-strand-bias = 0.95 (double, parameters json file)
3: snp-strand-bias-pval = 0.01 (double, parameters json file)
3: mnp-min-cov-each-strand = 4 (integer, parameters json file)
3: mnp-min-variant-score = 6 (double, parameters json file)
3: mnp-min-allele-freq = 0.02 (double, parameters json file)
3: mnp-min-coverage = 100 (integer, parameters json file)
3: mnp-strand-bias = 0.95 (double, parameters json file)
3: mnp-strand-bias-pval = 0.01 (double, parameters json file)
3: indel-min-cov-each-strand = 4 (integer, parameters json file)
3: indel-min-variant-score = 6 (double, parameters json file)
3: indel-min-allele-freq = 0.02 (double, parameters json file)
3: indel-min-coverage = 100 (integer, parameters json file)
3: indel-strand-bias = 0.9 (double, parameters json file)
3: indel-strand-bias-pval = 1 (double, parameters json file)
3: hotspot-min-cov-each-strand = 4 (integer, parameters json file)
3: hotspot-min-variant-score = 6 (double, parameters json file)
3: hotspot-min-allele-freq = 0.02 (double, parameters json file)
3: hotspot-min-coverage = 100 (integer, parameters json file)
3: hotspot-strand-bias = 0.95 (double, parameters json file)
3: hotspot-strand-bias-pval = 0.01 (double, parameters json file)
3: max-flows-to-test = 10 (integer, builtin default)
3: min-delta-for-flow = 0.1 (double, builtin default)
3: prediction-precision = 1 (double, parameters json file)
3: outlier-probability = 0.005 (double, parameters json file)
3: germline-prior-strength = 0 (double, builtin default)
3: heavy-tailed = 3 (integer, parameters json file)
3: filter-unusual-predictions = 0.12 (double, parameters json file)
3: soft-clip-bias-checker = 0.1 (double, builtin default)
3: filter-deletion-predictions = 0.2 (double, parameters json file)
3: filter-insertion-predictions = 0.2 (double, parameters json file)
3: max-detail-level = 0 (integer, builtin default)
3: shift-likelihood-penalty = 0.3 (double, builtin default)
3: minimum-sigma-prior = 0.085 (double, builtin default)
3: slope-sigma-prior = 0.0084 (double, builtin default)
3: sigma-prior-weight = 1 (double, builtin default)
3: k-zero = 3 (double, builtin default)
3: num-threads = 4 (integer, command line option)
3: num-variants-per-thread = 250 (integer, builtin default)
3: use-sse-basecaller = false (boolean, command line option)
3: do-json-diagnostic = false (boolean, builtin default)
3: do-minimal-diagnostic = false (boolean, builtin default)
3: process-input-positions-only = false (boolean, builtin default)
3: suppress-recalibration = false (boolean, parameters json file)
3: resolve-clipped-bases = false (boolean, builtin default)
3: prefix-exclude = 6
3: allow-indels = true (boolean, parameters json file)
3: allow-snps = true (boolean, parameters json file)
3: allow-mnps = true (boolean, parameters json file)
3: allow-complex = false (boolean, parameters json file)
3: left-align-indels = false (boolean, builtin default)
3: use-best-n-alleles = 2 (integer, builtin default)
3: use-input-allele-only = false (boolean, builtin default)
3: min-mapping-qv = 4 (integer, parameters json file)
3: read-snp-limit = 10 (integer, parameters json file)
3: read-max-mismatch-fraction = 1 (double, parameters json file)
3: max-complex-gap = 1 (integer, builtin default)
3: gen-min-alt-allele-freq = 0.01 (double, parameters json file)
3: gen-min-coverage = 6 (integer, parameters json file)
3: gen-min-indel-alt-allele-freq = 0.01 (double, parameters json file)
3: override-limits = false (boolean, builtin default)
3: Limit check parameter hp-max-length: lim. 1 <= 8? OK!
3: Limit check parameter sse-prob-threshold: lim. 0 <= 1 <= lim. 1? OK!
3: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK!
3: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK!
3: Limit check parameter realignment-threshold: lim. 0 <= 0 <= lim. 1? OK!
3: Limit check parameter data-quality-stringency: lim. 0 <= 10? OK!
3: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK!
3: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK!
3: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK!
3: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK!
3: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK!
3: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK!
3: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 4? OK!
3: Limit check parameter snp-min-variant-score: lim. 0 <= 6? OK!
3: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK!
3: Limit check parameter snp-min-coverage: lim. 0 <= 100? OK!
3: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
3: Limit check parameter snp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK!
3: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 4? OK!
3: Limit check parameter mnp-min-variant-score: lim. 0 <= 6? OK!
2/8 Test #4: tvcutils_call .................................... Passed 0.01 sec
test 6
Start 6: tvcutils_validate_bed_call
6: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "validate_bed"
6: Test timeout computed to be: 10000000
2: SampleManager: Found 1 read group(s) and 1 sample(s).
2: SampleManager: Primary sample "85" (default) present in 1 read group(s)
2: TVC found a total of 1 different flow orders of max flow lengths: 500
3: Limit check parameter 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 /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed
3: TargetsManager: 1 target(s)
3: TargetsManager: Trimming of AmpliSeq primers is enabled
3: SampleManager: Found 1 read group(s) and 1 sample(s).
3: SampleManager: Primary sample "85" (default) present in 1 read group(s)
3: TVC found a total of 1 different flow orders of max flow lengths: 500
5:
5: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
5:
5: Usage: tvcutils prepare_hotspots [options]
5:
5: General options:
5: -b,--input-bed FILE input is a hotspots BED file (either -b or -v required)
5: -v,--input-vcf FILE input is a hotspots VCF file (either -b or -v required)
5: -d,--output-bed FILE output left-aligned hotspots in BED format [none]
5: -o,--output-vcf FILE output is a hotspots VCF file. To be used as input to --hotspot-vcf argument of variant_caller_pipeline.py (recommended) [none]
5: -r,--reference FILE FASTA file containing reference genome (required)
5: -a,--left-alignment on/off perform left-alignment of indels [off]
5: -s,--allow-block-substitutions on/off do not filter out block substitution hotspots [on]
5: -u,--unmerged-bed FILE input a target bed file to filter out hotspots that contain a junction of 2 amplicons (optional)
5:
3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.01 sec
test 7
Start 7: tvcutils_unify_vcf_call
7: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "unify_vcf"
7: Test timeout computed to be: 10000000
6:
6: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
6:
6: Usage: tvcutils validate_bed [options]
6:
6: Input selection options (must provide one):
6: --target-regions-bed FILE input is a target regions BED file (required)
6: --hotspots-bed FILE input is a hotspots BED file (required)
6:
6: General options:
6: --reference FILE FASTA file containing reference genome (required)
6: --validation-log FILE log file for user-readable warning/error messages [stdout]
6: --meta-json FILE save validation and file statistics to json file [none]
6: --unmerged-detail-bed FILE output a valid unmerged BED. To be used as input to --primer-trim-bed argument of variant_caller_pipeline.py (recommended) [none]
6: --unmerged-plain-bed FILE output a valid merged BED. To be used as input to --region-bed argument of variant_caller_pipeline.py (recommended) [none]
6: --merged-detail-bed FILE output an (almost) valid bedDetail merged BED [none]
6: --merged-plain-bed FILE output a valid plain merged BED [none]
6: --effective-bed FILE output a valid effective BED [none]
6:
4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.01 sec
test 8
Start 8: tvcassembly_call
8: Test command: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcassembly
8: Test timeout computed to be: 10000000
7: Parameter novel-tvc-vcf is required and empty.
7:
7: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
7:
7: Usage: tvcutils unify_vcf [options]
7:
7: General options:
7: -t,--novel-tvc-vcf FILE small variants VCF file produced by TVC (required)
7: -i,--novel-assembly-vcf FILE long indels VCF file produced by TVCASSEMBLY (optional)
7: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional)
7: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional)
7: -f,--reference-fasta FILE FASTA file containing reference genome (required)
7: -b,--target-file FILE target regions BED file (optional)
7: -o,--output-vcf FILE output merged and annotated VCF or VCF.GZ file (required)
7: -j,--tvc-metrics FILE JSON file with tvc metrics (optional)
7: -d,--input-depth FILE output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok)
7: -m,--min-depth INT minimum coverage depth in GVCF output (optional)
7:
5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.01 sec
8: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly
8:
8: Usage: tvcassembly [options]
8:
8: General options:
8: -h,--help print this help message and exit
8: -v,--version print version and exit
8: -n,--num-threads INT number of worker threads [2]
8: --parameters-file FILE json file with algorithm control parameters [optional]
8: -r,--reference FILE reference fasta file [required]
8: -b,--input-bam FILE bam file with mapped reads [required]
8: -t,--target-file FILE only process targets in this bed file [optional]
8: -o,--output-vcf FILE vcf file with variant calling results [required]
8: -g,--sample-name STRING sample for which variants are called (In case of input BAM files with multiple samples) [optional if there is only one sample]
8: --force-sample-name STRING force all read groups to have this sample name [off]
8:
8: --kmer_len INT (klen) Size of the smallest k-mer used in assembly [19].
8: --min_var_count INT (mincount) Minimum support for a variant to be evaluated [5].
8: --short_suffix_match INT (ssm) Minimum sequence match on both sides of the variant [5].
8: --min_indel_size INT (mis) Minimum size indel reported by assembly [4].
8: --max_hp_length INT (maxhp) Variants containing HP larger than this are not reported [8].
8: --min_var_freq FLOAT (minfreq) Minimum frequency of the variant to be reported [0.15].
8: --min_var_score FLOAT (minscore) Minimum score of the variant to be reported [10].
8: --relative_strand_bias FLOAT (stbias) Variants with strand bias above this are not reported [0.80].
8: --output_mnv INT (mnv) Output multi-nucleotide variants assembled in a region with multiple adjacent variants [0].
8:
6/8 Test #8: tvcassembly_call ................................. Passed 0.01 sec
2: Recalibration was detected from comment lines in bam file(s):
2: 1 unique blocks of recalibration info detected.
2: Loading systematic error contexts.
3: Recalibration was detected from comment lines in bam file(s):
3: 1 unique blocks of recalibration info detected.
3: Loading systematic error contexts.
3: Loaded.
2: Loaded.
2: Recalibration model: suppressed
2:
2:
2: [tvc] Normal termination. Processing time: 1 seconds.
3:
3:
3: [tvc] Normal termination. Processing time: 1 seconds.
7/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 3.36 sec
8/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 3.37 sec
100% tests passed, 0 tests failed out of 8
Total Test time (real) = 3.37 sec
make[1]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install --destdir=debian/tvc/ -a
cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<<BUILDDIR>>/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -B/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/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 '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/tvcutils.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/tvc.dir/DependInfo.cmake --color=
Consolidate compiler generated dependencies of target tvcassembly
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'.
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
Consolidate compiler generated dependencies of target tvcutils
[ 10%] Built target tvcassembly
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'.
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
[ 31%] Built target tvcutils
Consolidate compiler generated dependencies of target tvc
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build
make[3]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'.
make[3]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
[100%] Built target tvc
make[2]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed
-- Installing: /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed
make[1]: Leaving directory '/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf'
dh_installdocs -a
dh_installchangelogs -a
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/tvc/usr/bin/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/tvc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcutils 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/tvc debian/tvc/usr/bin/tvcutils 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/tvc debian/tvc/usr/bin/tvcutils 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+b2_armhf.deb'.
dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../tvc_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../tvc_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-06-18T17:16:12Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
tvc_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.changes:
------------------------------------------------------
Format: 1.8
Date: Sun, 31 Oct 2021 20:30:30 +0530
Source: tvc (5.0.3+git20151221.80e144e+dfsg-4)
Binary: tvc tvc-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 5.0.3+git20151221.80e144e+dfsg-4+b2
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
tvc - genetic variant caller for Ion Torrent sequencing platforms
Changes:
tvc (5.0.3+git20151221.80e144e+dfsg-4+b2) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
65cd84918f94f945ef9db37907a86389c683fa2d 10889020 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.deb
284f48a239f70be9f7e17def2dd24f619863e60a 7706 tvc_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.buildinfo
0c1170f80f475ae5f5e8cd6f505d667bb21c0e31 936088 tvc_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.deb
Checksums-Sha256:
4990372decc06757948d85511b06daf610c8463c5d484b607232f9e84f038729 10889020 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.deb
e80dd7aa1b87b314b3495836eb1c9b00dc93a92eeb3d3377cfbeb4055bff500d 7706 tvc_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.buildinfo
ce23b80214866de16c94c7320dccaf3f8624afceedfdb116770f6d78170f8ad5 936088 tvc_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.deb
Files:
66020b6e2759319cf513f54a9d49f1f8 10889020 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.deb
9525c6a909a1bcfa82ec2553a8f7aea9 7706 science optional tvc_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.buildinfo
d353fa98ce0b3ea3af11be82c1b135bd 936088 science optional tvc_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.deb
--------------------------------------------------------
new Debian package, version 2.0.
size 10889020 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+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10945
Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-4+b2)
Section: debug
Priority: optional
Description: debug symbols for tvc
Build-Ids: 7f8b576f384094c1637dac02a335fbe3874d5f74 c23fc83ed8e2c1d4064098e10eea89ca502a6135 d42f839411a0d0b6bd94b1510fcb6f577fda91b5
drwxr-xr-x root/root 0 2021-10-31 15:00 ./
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.build-id/7f/
-rw-r--r-- root/root 801100 2021-10-31 15:00 ./usr/lib/debug/.build-id/7f/8b576f384094c1637dac02a335fbe3874d5f74.debug
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.build-id/c2/
-rw-r--r-- root/root 7661968 2021-10-31 15:00 ./usr/lib/debug/.build-id/c2/3fc83ed8e2c1d4064098e10eea89ca502a6135.debug
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.build-id/d4/
-rw-r--r-- root/root 2249748 2021-10-31 15:00 ./usr/lib/debug/.build-id/d4/2f839411a0d0b6bd94b1510fcb6f577fda91b5.debug
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 477444 2021-10-31 15:00 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/tvc.debug
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-31 15:00 ./usr/share/doc/tvc-dbgsym -> tvc
tvc_5.0.3+git20151221.80e144e+dfsg-4+b2_armhf.deb
-------------------------------------------------
new Debian package, version 2.0.
size 936088 bytes: control archive=1728 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+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2958
Depends: libarmadillo11 (>= 1:11.1.1+dfsg), libbamtools2.5.1 (>= 2.5.1+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 2021-10-31 15:00 ./
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/bin/
-rwxr-xr-x root/root 917536 2021-10-31 15:00 ./usr/bin/tvc
-rwxr-xr-x root/root 174404 2021-10-31 15:00 ./usr/bin/tvcassembly
-rwxr-xr-x root/root 485968 2021-10-31 15:00 ./usr/bin/tvcutils
-rwxr-xr-x root/root 12985 2021-10-31 15:00 ./usr/bin/variant_caller_pipeline.py
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/examples/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/examples/example1/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/examples/example1/expected/
-rw-r--r-- root/root 6876 2015-12-21 20:38 ./usr/share/TVC/examples/example1/expected/TSVC_variants.vcf
-rw-r--r-- root/root 6479 2015-12-21 20:38 ./usr/share/TVC/examples/example1/expected/small_variants.vcf
-rw-r--r-- root/root 108 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.dict
-rw-r--r-- root/root 3400 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.fasta
-rw-r--r-- root/root 22 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.fasta.fai
-rw-r--r-- root/root 225904 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bam
-rw-r--r-- root/root 96 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bam.bai
-rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bed
-rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_merged_plain.bed
-rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_original.bed
-rw-r--r-- root/root 70 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_unmerged_detail.bed
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/pluginMedia/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/pluginMedia/parameter_sets/
-rw-r--r-- root/root 2809 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2926 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2826 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json
-rw-r--r-- root/root 2918 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json
-rw-r--r-- root/root 3062 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2628 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json
-rw-r--r-- root/root 2757 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/TVC/sse/
-rw-r--r-- root/root 683778 2015-12-21 20:38 ./usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt
-rw-r--r-- root/root 451754 2015-12-21 20:38 ./usr/share/TVC/sse/motifset.txt
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/doc/tvc/
-rw-r--r-- root/root 1078 2021-10-31 14:47 ./usr/share/doc/tvc/README.Debian
-rw-r--r-- root/root 234 2021-10-31 15:00 ./usr/share/doc/tvc/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1240 2021-10-31 15:00 ./usr/share/doc/tvc/changelog.Debian.gz
-rw-r--r-- root/root 2939 2021-10-31 14:47 ./usr/share/doc/tvc/copyright
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/lintian/
drwxr-xr-x root/root 0 2021-10-31 15:00 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 135 2021-10-31 14:47 ./usr/share/lintian/overrides/tvc
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 140532
Build-Time: 216
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 407
Job: tvc_5.0.3+git20151221.80e144e+dfsg-4
Machine Architecture: armhf
Package: tvc
Package-Time: 643
Source-Version: 5.0.3+git20151221.80e144e+dfsg-4
Space: 140532
Status: successful
Version: 5.0.3+git20151221.80e144e+dfsg-4+b2
--------------------------------------------------------------------------------
Finished at 2022-06-18T17:16:12Z
Build needed 00:10:43, 140532k disk space