Raspbian Package Auto-Building

Build log for tvc (5.0.3+git20151221.80e144e+dfsg-3+b1) on armhf

tvc → 5.0.3+git20151221.80e144e+dfsg-3+b1 → armhf → 2020-10-25 20:45:44 

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02

+=================================================================================+
| tvc 5.0.3+git20151221.80e144e+dfsg-3+b1 (armhf) Sun, 25 Oct 2020 20:34:38 +0000 |
+=================================================================================+

Package: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-3+b1
Source Version: 5.0.3+git20151221.80e144e+dfsg-3
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-164a9246-b3e1-40e8-a258-fac80b513c3b' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.5 MB in 9s (2707 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'tvc' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/tvc.git
Please use:
git clone https://salsa.debian.org/med-team/tvc.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 756 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (dsc) [2200 B]
Get:2 http://172.17.0.1/private bullseye-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (tar) [745 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (diff) [8968 B]
Fetched 756 kB in 1s (1355 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/tvc-gwPQlq/tvc-5.0.3+git20151221.80e144e+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/tvc-gwPQlq' 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-KSITek/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-KSITek/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-KSITek/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-KSITek/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-KSITek/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-KSITek/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-KSITek/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-KSITek/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (9475 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  bsdextrautils krb5-locales libpam-cap 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 0 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-KSITek/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (63.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12710 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-KSITek/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-KSITek/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-KSITek/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-KSITek/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-KSITek/apt_archive ./ Sources [535 B]
Get:5 copy:/<<BUILDDIR>>/resolver-KSITek/apt_archive ./ Packages [618 B]
Fetched 2486 B in 0s (11.2 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 packages were automatically installed and are no longer required:
  krb5-locales libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev cmake cmake-data debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base hdf5-helpers intltool-debian libaec-dev libaec0
  libarchive-zip-perl libarchive13 libarmadillo-dev libarmadillo10 libarpack2
  libarpack2-dev libbamtools-dev libbamtools2.5.1 libblas-dev libblas3
  libboost-math-dev libboost-math1.71-dev libboost-math1.71.0 libboost1.71-dev
  libbrotli1 libcroco3 libcurl4 libdebhelper-perl libdisorder-dev libdisorder0
  libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
  libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
  libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu67
  libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev libjsoncpp1
  liblapack-dev liblapack3 libmagic-mgc libmagic1 libncurses6 libnghttp2-14
  libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2
  libsmithwaterman-dev libsmithwaterman0 libssh2-1 libsub-override-perl
  libsuperlu-dev libsuperlu5 libsz2 libtool libuchardet0 libuv1 libxml2 m4
  man-db po-debconf procps zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make
  gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libitpp-dev
  libbamtools-doc liblapack-doc libboost1.71-doc libboost-atomic1.71-dev
  libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev
  libboost-contract1.71-dev libboost-coroutine1.71-dev
  libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev
  libboost-filesystem1.71-dev libboost-graph1.71-dev
  libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev
  libboost-locale1.71-dev libboost-log1.71-dev libboost-mpi1.71-dev
  libboost-mpi-python1.71-dev libboost-numpy1.71-dev
  libboost-program-options1.71-dev libboost-python1.71-dev
  libboost-random1.71-dev libboost-regex1.71-dev
  libboost-serialization1.71-dev libboost-stacktrace1.71-dev
  libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev
  libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev
  libboost1.71-tools-dev libmpfrc++-dev libntl-dev libhdf5-doc libsuperlu-doc
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
  www-browser libmail-box-perl
Recommended packages:
  curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs libgpm2 publicsuffix libltdl-dev
  libmail-sendmail-perl psmisc
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev cmake cmake-data debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base hdf5-helpers intltool-debian libaec-dev libaec0
  libarchive-zip-perl libarchive13 libarmadillo-dev libarmadillo10 libarpack2
  libarpack2-dev libbamtools-dev libbamtools2.5.1 libblas-dev libblas3
  libboost-math-dev libboost-math1.71-dev libboost-math1.71.0 libboost1.71-dev
  libbrotli1 libcroco3 libcurl4 libdebhelper-perl libdisorder-dev libdisorder0
  libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
  libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
  libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu67
  libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp-dev libjsoncpp1
  liblapack-dev liblapack3 libmagic-mgc libmagic1 libncurses6 libnghttp2-14
  libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2
  libsmithwaterman-dev libsmithwaterman0 libssh2-1 libsub-override-perl
  libsuperlu-dev libsuperlu5 libsz2 libtool libuchardet0 libuv1 libxml2 m4
  man-db po-debconf procps sbuild-build-depends-tvc-dummy zlib1g-dev
0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded.
Need to get 45.9 MB of archives.
After this operation, 297 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-KSITek/apt_archive ./ sbuild-build-depends-tvc-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20200918-1 [79.5 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-5 [59.8 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-5 [238 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.18.2-1+rpi1 [1725 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.1 [578 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2 [259 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.41.0-3 [63.0 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.72.0-1 [300 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp1 armhf 1.7.4-3.1 [65.8 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.4.0-1 [133 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.39.0-1 [118 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.18.2-1+rpi1 [3130 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.181-1 [161 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.1-2 [1174 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf hdf5-helpers armhf 1.10.6+repack-2 [40.0 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libaec0 armhf 1.0.4-1 [20.0 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libsz2 armhf 1.0.4-1 [6664 B]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libaec-dev armhf 1.0.4-1 [17.8 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.0-13+rpi1 [231 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libarpack2 armhf 3.7.0-3 [85.7 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libsuperlu5 armhf 5.2.2+dfsg1-2 [128 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libarmadillo10 armhf 1:10.1.0+dfsg-2 [95.8 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libarpack2-dev armhf 3.7.0-3 [96.2 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-103-1 armhf 1.10.6+repack-2 [1184 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-fortran-102 armhf 1.10.6+repack-2 [93.0 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-100 armhf 1.10.6+repack-2 [78.1 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.6+repack-2 [49.8 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.6+repack-2 [128 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.6+repack-2 [36.9 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:2.0.5-1.1 [121 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:2.0.5-1.1 [241 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:2.0.5-1.1 [66.0 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-dev armhf 1.10.6+repack-2 [2167 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libsuperlu-dev armhf 5.2.2+dfsg1-2 [21.4 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libarmadillo-dev armhf 1:10.1.0+dfsg-2 [386 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-7 [133 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-7 [180 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libboost1.71-dev armhf 1.71.0-7 [9098 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libboost-math1.71.0 armhf 1.71.0-7 [348 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libboost-math1.71-dev armhf 1.71.0-7 [468 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libboost-math-dev armhf 1.71.0.3+b3 [4604 B]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-1 [4568 B]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-1 [4156 B]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-9 [33.0 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-9 [36.8 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp-dev armhf 1.7.4-3.1 [81.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libhdf5-hl-cpp-100:armhf (1.10.6+repack-2) ...
Setting up libhdf5-fortran-102:armhf (1.10.6+repack-2) ...
Setting up cmake (3.18.2-1+rpi1) ...
Setting up libhdf5-hl-fortran-100:armhf (1.10.6+repack-2) ...
Setting up po-debconf (1.0.21) ...
Setting up libhdf5-dev (1.10.6+repack-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libarmadillo-dev (1:10.1.0+dfsg-2) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2.1) ...
Setting up sbuild-build-depends-tvc-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-13+rpi1 gcc-10_10.2.0-13+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc1-2 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 cmake_3.18.2-1+rpi1 cmake-data_3.18.2-1+rpi1 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-13+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-13+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-13+rpi1 gcc-10-base_10.2.0-13+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hdf5-helpers_1.10.6+repack-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.17-10 libacl1_2.2.53-8 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libarmadillo-dev_1:10.1.0+dfsg-2 libarmadillo10_1:10.1.0+dfsg-2 libarpack2_3.7.0-3 libarpack2-dev_3.7.0-3 libasan6_10.2.0-13+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-13+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libbamtools-dev_2.5.1+dfsg-7 libbamtools2.5.1_2.5.1+dfsg-7 libbinutils_2.35.1-2+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-7 libboost-math-dev_1.71.0.3+b3 libboost-math1.71-dev_1.71.0-7 libboost-math1.71.0_1.71.0-7 libboost1.71-dev_1.71.0-7 libbrotli1_1.0.9-2 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.0-13+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libcurl4_7.72.0-1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdisorder-dev_0.0.2+git20130809.8062ee1-1 libdisorder0_0.0.2+git20130809.8062ee1-1 libdpkg-perl_1.20.5+rpi1 libelf1_0.181-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-13+rpi1 libgcc-s1_10.2.0-13+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgfortran5_10.2.0-13+rpi1 libglib2.0-0_2.66.1-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-13+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libhdf5-103-1_1.10.6+repack-2 libhdf5-cpp-103-1_1.10.6+repack-2 libhdf5-dev_1.10.6+repack-2 libhdf5-fortran-102_1.10.6+repack-2 libhdf5-hl-100_1.10.6+repack-2 libhdf5-hl-cpp-100_1.10.6+repack-2 libhdf5-hl-fortran-100_1.10.6+repack-2 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjpeg-dev_1:2.0.5-1.1 libjpeg62-turbo_1:2.0.5-1.1 libjpeg62-turbo-dev_1:2.0.5-1.1 libjsoncpp-dev_1.7.4-3.1 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.53+dfsg-1+rpi1 libldap-common_2.4.53+dfsg-1+rpi1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libprocps8_2:3.3.16-5 libpsl5_0.21.0-1.1 libreadline8_8.0-4 librhash0_1.4.0-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.4-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsmithwaterman-dev_0.0+git20160702.2610e25-9 libsmithwaterman0_0.0+git20160702.2610e25-9 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 libsub-override-perl_0.09-2 libsuperlu-dev_5.2.2+dfsg1-2 libsuperlu5_5.2.2+dfsg1-2 libsystemd0_246.4-1+rpi1 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-13+rpi1 libuchardet0_0.0.7-1 libudev1_246.4-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libuv1_1.39.0-1 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6.1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 procps_2:3.3.16-5 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-tvc-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020d-1 util-linux_2.36-3 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

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


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.Yw8Vc5Um/trustedkeys.kbx': General error
gpgv: Signature made Sun Mar  1 05:51:37 2020 UTC
gpgv:                using RSA key 90E2D2C1AD146A1B7EBB891DBBC17EBB1396F2F7
gpgv:                issuer "stuart@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./tvc_5.0.3+git20151221.80e144e+dfsg-3.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-3.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

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

Sufficient free space for build

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

Created changelog entry for binNMU version 5.0.3+git20151221.80e144e+dfsg-3+b1

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-164a9246-b3e1-40e8-a258-fac80b513c3b
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-3+b1
dpkg-buildpackage: info: source distribution bullseye-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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf ..
-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- 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 -fdebug-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_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"
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/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend
make  -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend
make  -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.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/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/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/tvc.dir/DependInfo.cmake --color=
Scanning 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'
Scanning dependencies of target tvcutils
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'
[  3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o
[  3%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp
[  4%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/tvcutils.cpp
Scanning 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
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[  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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp
[ 10%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.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:349,
                 from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:90:1: note: declared here
   90 | set_stream_err1(std::ostream& user_stream)
      | ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:37: 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:349,
                 from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:90:1: note: declared here
   90 | 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:349,
                 from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:101:1: note: declared here
  101 | set_stream_err2(std::ostream& user_stream)
      | ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:37: 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:349,
                 from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:101:1: note: declared here
  101 | set_stream_err2(std::ostream& user_stream)
      | ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/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++/10/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++/10/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++/10/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 12%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp
[ 14%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/IonVersion.cpp
[ 15%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/validate_bed.cpp
In file included from /usr/include/string.h:495,
                 from /usr/include/c++/10/cstring:42,
                 from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:12:
In function 'char* strncpy(char*, const char*, size_t)',
    inlined from 'char* GetProcessParam(const char*, const char*)' at /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:503:15:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp: In function 'char* GetProcessParam(const char*, const char*)':
/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:503:37: note: length computed here
  503 |       strncpy (keyword, buf, strlen (buf)-1);
      |                              ~~~~~~~^~~~~
[ 17%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp
[ 18%] Linking CXX executable tvcassembly
/usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-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'
[ 18%] Built target tvcassembly
[ 20%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp
[ 21%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/BAMWalkerEngine.cpp
[ 23%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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++/10/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++/10/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++/10/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++/10/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 25%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/OrderedBAMWriter.cpp
[ 26%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp
[ 28%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp
In file included from /usr/include/c++/10/vector:72,
                 from /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:13:
/usr/include/c++/10/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++/10/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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator<markov_state>]':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/bits/vector.tcc: In member function 'void markov_chain<T>::generate_states(T, T) [with T = unsigned int]':
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 29%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp
[ 31%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp
[ 32%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp
[ 34%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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:336:35: 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;
      |                                   ^~~~~~~~
[ 35%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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:678:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
  678 |  fread(buf, 1, 28, fp->file);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 37%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/IonVersion.cpp
[ 39%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HandleVariant.cpp
[ 40%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HotspotReader.cpp
[ 42%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/MetricsManager.cpp
[ 43%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/MiscUtil.cpp
[ 45%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/ExtendParameters.cpp
[ 46%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp
[ 48%] Linking CXX executable tvcutils
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/usr/bin/c++ -g -O2 -fdebug-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'
[ 48%] Built target tvcutils
[ 50%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/VcfFormat.cpp
[ 51%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads/ExtendedReadInfo.cpp
In file included from /usr/include/c++/10/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++/10/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++/10/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++/10/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++/10/bits/stl_vector.h: In constructor 'PersistingThreadObjects::PersistingThreadObjects(const InputStructures&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 53%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ErrorMotifs.cpp
[ 54%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/LocalContext.cpp
[ 56%] 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ClassifyVariant.cpp
[ 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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
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[ 68%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o
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[ 76%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o
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[ 78%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/split.cpp.o
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[ 79%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o
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[ 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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:336:35: 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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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:678:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
  678 |  fread(buf, 1, 28, fp->file);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
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/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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/DPTreephaser.cpp
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/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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.cpp
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/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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/FlowAlignment.cpp
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/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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o -c /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp
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/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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fdebug-prefix-map=/<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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++/10/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++/10/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++/10/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++/10/bits/vector.tcc: In member function 'void OptArgs::StringToDoubleVector(std::vector<double>&, const string&, const string&, char)':
/usr/include/c++/10/bits/vector.tcc:121:21: 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 -fdebug-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 
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	cd obj-arm-linux-gnueabihf && make -j4 test 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 -j4
Test project /<<BUILDDIR>>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf
    Start 1: tvc_call
    Start 2: tvc_test_1_thread_sse_off
    Start 3: tvc_test_4_threads_sse_off_with_parameter_file
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1/8 Test #1: tvc_call .........................................   Passed    0.02 sec
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2/8 Test #4: tvcutils_call ....................................   Passed    0.01 sec
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100% tests passed, 0 tests failed out of 8

Total Test time (real) =   3.50 sec
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[ 20%] Built target tvcassembly
[ 31%] Built target tvcutils
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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/tvc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcassembly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: 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/tvc debian/tvc/usr/bin/tvcutils were not linked against libdisorder.so.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc debian/tvc/usr/bin/tvcassembly debian/tvc/usr/bin/tvcutils were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.deb'.
dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../tvc_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-10-25T20:45:37Z

Finished
--------

I: Built successfully

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


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


tvc_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.changes:
------------------------------------------------------

Format: 1.8
Date: Sun, 01 Mar 2020 15:57:45 +1100
Source: tvc (5.0.3+git20151221.80e144e+dfsg-3)
Binary: tvc tvc-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 5.0.3+git20151221.80e144e+dfsg-3+b1
Distribution: bullseye-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-3+b1) bullseye-staging; urgency=low, binary-only=yes
 .
   * Binary-only non-maintainer upload for armhf; no source changes.
   * rebuild due to debcheck failure
Checksums-Sha1:
 3dfbb9f1f781363ee86b5c60c353bb3f56776c16 10205452 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.deb
 9b0a643dcefb3ecabd65c4eb96f9efa488cc91f8 7491 tvc_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.buildinfo
 6508afe73669bd9d67738b60c0476146afbd094c 939120 tvc_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.deb
Checksums-Sha256:
 c6070c0f44ab1a8ea476cd90b205a40ac26adc8982415d0dc0bb5e2fdd0c2fc3 10205452 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.deb
 38ee6498c2293c4e4d9e456312ef8625fb6b32a0ce1aeb2895644c4072fcf78f 7491 tvc_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.buildinfo
 158b030c9a3c86f04d9fad3b77f0733cde9df356cfa1331ca3fbc957235d380e 939120 tvc_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.deb
Files:
 4eef8394a13d64ede7ce405a7096e7d3 10205452 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.deb
 84b2f29bbfcaeaa589067439b4e52b8b 7491 science optional tvc_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.buildinfo
 7073e218cca51eb90820453268cf269d 939120 science optional tvc_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.deb

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


tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.deb
--------------------------------------------------------

 new Debian package, version 2.0.
 size 10205452 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-3)
 Version: 5.0.3+git20151221.80e144e+dfsg-3+b1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 10349
 Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-3+b1)
 Section: debug
 Priority: optional
 Description: debug symbols for tvc
 Build-Ids: 2eb9ae5541f2c4784eac3c72d02bdcdd009ecd6c 75b043734dbf4e1d1339c10cd723647c6ea1e697 92814261b9ea5fc3e3e75a4463135201a6800728

drwxr-xr-x root/root         0 2020-03-01 04:57 ./
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/lib/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/lib/debug/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/lib/debug/.build-id/2e/
-rw-r--r-- root/root   7132560 2020-03-01 04:57 ./usr/lib/debug/.build-id/2e/b9ae5541f2c4784eac3c72d02bdcdd009ecd6c.debug
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/lib/debug/.build-id/75/
-rw-r--r-- root/root   2231416 2020-03-01 04:57 ./usr/lib/debug/.build-id/75/b043734dbf4e1d1339c10cd723647c6ea1e697.debug
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/lib/debug/.build-id/92/
-rw-r--r-- root/root    769876 2020-03-01 04:57 ./usr/lib/debug/.build-id/92/814261b9ea5fc3e3e75a4463135201a6800728.debug
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root    447020 2020-03-01 04:57 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/tvc.debug
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/share/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-03-01 04:57 ./usr/share/doc/tvc-dbgsym -> tvc


tvc_5.0.3+git20151221.80e144e+dfsg-3+b1_armhf.deb
-------------------------------------------------

 new Debian package, version 2.0.
 size 939120 bytes: control archive=1724 bytes.
    1044 bytes,    17 lines      control              
    2537 bytes,    29 lines      md5sums              
 Package: tvc
 Source: tvc (5.0.3+git20151221.80e144e+dfsg-3)
 Version: 5.0.3+git20151221.80e144e+dfsg-3+b1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 2982
 Depends: libarmadillo10 (>= 1:10.1.0+dfsg), libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.29), libdisorder0 (>= 0.0.2), libgcc-s1 (>= 3.5), libjsoncpp1 (>= 1.7.4), libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 5.2), 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 2020-03-01 04:57 ./
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/bin/
-rwxr-xr-x root/root    921624 2020-03-01 04:57 ./usr/bin/tvc
-rwxr-xr-x root/root    174400 2020-03-01 04:57 ./usr/bin/tvcassembly
-rwxr-xr-x root/root    506460 2020-03-01 04:57 ./usr/bin/tvcutils
-rwxr-xr-x root/root     12985 2020-03-01 04:57 ./usr/bin/variant_caller_pipeline.py
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/share/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/share/TVC/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/share/TVC/examples/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/share/TVC/examples/example1/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./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 2020-03-01 04:57 ./usr/share/TVC/pluginMedia/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./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 2020-03-01 04:57 ./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 2020-03-01 04:57 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/share/doc/tvc/
-rw-r--r-- root/root      1078 2020-03-01 04:46 ./usr/share/doc/tvc/README.Debian
-rw-r--r-- root/root       236 2020-03-01 04:57 ./usr/share/doc/tvc/changelog.Debian.armhf.gz
-rw-r--r-- root/root      1180 2020-03-01 04:57 ./usr/share/doc/tvc/changelog.Debian.gz
-rw-r--r-- root/root      2939 2020-03-01 04:46 ./usr/share/doc/tvc/copyright
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/share/lintian/
drwxr-xr-x root/root         0 2020-03-01 04:57 ./usr/share/lintian/overrides/
-rw-r--r-- root/root       135 2020-03-01 04:46 ./usr/share/lintian/overrides/tvc


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


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

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

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

Build Architecture: armhf
Build-Space: 145484
Build-Time: 242
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 399
Job: tvc_5.0.3+git20151221.80e144e+dfsg-3
Machine Architecture: armhf
Package: tvc
Package-Time: 659
Source-Version: 5.0.3+git20151221.80e144e+dfsg-3
Space: 145484
Status: successful
Version: 5.0.3+git20151221.80e144e+dfsg-3+b1
--------------------------------------------------------------------------------
Finished at 2020-10-25T20:45:37Z
Build needed 00:10:59, 145484k disk space